ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...attcaccagagttaaccttttgtaatagcctgcaacttgaatacaaggtcacagaaaatatccactcatgaactgctatttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTCATCAGCAGCGC

Basic information

species	Zea mays
transcript	GRMZM2G104373_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 5

-------------------------------------------------------------------attcaccaga-gttaaccttttgtaat--------agcctgcaacttgaatacaaggtcacagaaaatat-ccactcatgaactgctattttta----------ttttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTCATCAGCAGCGC--
                                                                       || |   |  || | |||   ||           ||||     ||| | |    ||  |||   |   |  |  || ||| || ||||||          | ||||||||| |||||| || ||||| || ||||||||||||||||| ||||| |||||||||||||| ||||| || ||||| || || ||||||||||||  |||  |  | |  
gtaactcagctttgttttctcaaccagactccttgctctctagtactgttaatgttaaaactttcgagcatactaagtgccaatcctttcagatctgagtttgagctgcgctcagaacatatttgcatggaatgcaagtctttgttgcacttctctttttacatttgctgttcttctgttgctttagGTGACACATGCCGATTTCAAGAAGGCCAAAGAGAAGGTCATGTTCAAGAAGAAGGAAGGTGTACCGGAAGGGCTTTATATGTGAGAC--ATCCACCACTCAT

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 5

attcaccagagttaaccttttgta---atagcctgcaacttgaatacaaggtcacagaaaatatccactcatgaactgctatttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTC-ATCAGCAGCGC
  |    |  ||  | |||| ||    || |  |  ||  | |||   | ||            | | | ||||  |  | ||  ||||   | ||   | |||| || ||||| ||||| ||||||||||| || || || ||||| |||||||||||||| ||||| || || || ||||||||| |  | |||  |     
--tgtttaatgtgtatctttggtttgtattgtatataatat-aatttgaagttttttttctccccaatttatgatatcttcttactattacttttttgttcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAATACTATCCTCTATC-

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 5

-----attcaccagagttaaccttttgtaatagcctgcaacttgaatacaaggtcacagaaaatatccac-tcatgaactgctatttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGAC-TCATCAGCAGCGC
     |||||      |     |||| |  |    |||| |||   |    |||         || || | | |  || |||| ||||| || |||    | | |||| |||||||| ||||| |||||||| || || || |||||||| |||||||||||||| ||||| || || || |||||||||  | || ||| ||    
tttatattcaattttctctgtattttattttgttttgcaccttttttgagtggt------gtgtaccctcgtgaccaaatgcttttttttttatcttgctcttcagGTGACGCATGCCGACTTTAAGAAGGCAAAGGATAAAGTTATGTTTAAGAAGAAAGAAGGAGTGCCCGAAGGACTGTATATGTGAAGCATCTTCATCAATT-

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 5

attcaccagagttaaccttttgtaatagcctgcaacttgaatacaag-gtcacagaaaatatccactcatgaactgctatttttatttt-----ctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGAC-TCATCAGCAGCGC
       || | |    ||||||  |   |      ||| |     | ||  |      | | | ||||||| |   | ||||| ||||     ||    | | |||| |||||||| |||||||||||||| || || ||||||||||| |||||||||||||| ||||| || || || |||||||||  | || ||| ||    
------aagtgatcctattttgttttctacctttttttggaggggtgtgtgtcttttcctttactctcatgaccaaatgttttttttttaaaatcttgctcttcagGTGACGCATGCCGACTTCAAGAAGGCAAAGGATAAGGTTATGTTTAAGAAGAAAGAAGGGGTGCCAGAAGGACTGTATATGTGAAGCATCTTCATCATTT-

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 5

attcaccagagttaaccttttgtaatagcctgcaacttgaatacaaggtcacagaaaatatcc---------actcatgaactgctatttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTC-ATCAGCAGCGC
       |  ||| | ||| | |  | || || |  |||  || ||  | |    || | |           | | ||||  |  | ||  ||||     ||  || |||| || ||||| ||||| ||||||||||| || || || ||||| |||||||||||||| ||||| || || || ||||||||| |  | |||  |     
------taatgtttatcttctctt-tggcttgta--ttgtttataatataatttgaagtttttttctccccaatttatgatatcttcttactattactattttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAAACTATCCTCTATT-

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5

------attcaccagagttaaccttttgtaatagcctgca-acttgaatacaaggtcacagaaaatatccactcatga-actgctatttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTCATCAGCAGCGC-
      | ||   |   || |  |   | |    |   || ||    | |||        | || ||    |   |||  ||  | | ||||  ||   ||   | |||| || ||| | || |||||||| || || || ||||||||||||||||||||||||||||| || || ||||| || |||| | | | || | ||   | 
gtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAA-TTATAATCATATCG

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5

attcaccagagttaaccttttgtaatagcctgcaacttgaatacaaggtcacaga----aaatatccactcatgaactgctatttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTCATCAGCAGCGC--
          || |   || | |     |   | |||||| |    |  | ||       ||||      | | |||   | |||   | |||| |||  |||||| |||||||  |||||||||||||| || || |||||||||||||||||||||||||| || || || || || || ||||||   | ||   || ||   
----------gtaaggattctctggcttctcaccacttgattcatcgaacgcaatctttgaataattttactttaacctttgtttg-gtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAA--TGATGCACAACGACT

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5

attcaccagagttaa---ccttttgtaatagcctgcaacttgaatacaaggtcacagaaaatatccactcatgaactgctattt-ttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTCATCAGCAGCGC--
         |||| |   | ||   | |   | ||     ||| |  |    |  || |        |  || || |   | |  |||  | |||| || | |||| || |||| ||||||||||||||| || || ||||| |||||||||||||||||||| ||||| || || || || |||||| |     | ||  |    
---ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggaccaggatcccaattaaatttgactggttaaatactgt-gcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAAC--ACTGCTACATAT

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 5

attcaccagagttaaccttttgtaatagcctgcaacttgaatacaaggtcacagaaaatatccactcatgaactgctatttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTCATCAGCAGCGC
                                             || |    ||   | | |||   |    |  | |    |||||||  | |   ||||||| || || || ||||||||||| ||||| ||||| |||| |||||||||||||||||| ||||||||||| || |||| |    |     ||||  
-------------------------------------------gtagtttctcgatgcttttcacaact---ttcttgtaacgattttcttcttctccagGTAACTCAAGCTGATTTCAAGAAGGCGAAAGAGAAGGTCATGTACAAGAAGAAAGAAGGCGTCCCGGAGGGCCTGTACATGTAAATAGCCGTCCCAGCTT

upper sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 5

attcaccagagttaaccttttgtaatagcctgcaacttgaatacaaggtcacagaaaatatccactcatgaactgct-atttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAG-ACTCATCAGCAGCGC
                                               ||  |  ||    |    |||  |  | ||  |    |||||||  | |   ||||||| || || || ||||||||||| ||||| ||||| |||| |||||||||||||||||| ||||||||||| || |||| |  |  ||||  ||||  
--------------------------------------------gtagtttctcaatgcttt---tcacaactttcttgtaacgattttcttcttctccagGTAACTCAAGCTGATTTCAAGAAGGCGAAAGAGAAGGTCATGTACAAGAAGAAAGAAGGCGTCCCGGAGGGCCTGTACATGTAAATAGCCATCC-CAGCTT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|149110574|gb|EE294195.2|EE294195

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|37401158|gb|CF637942.1|CF637942

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|5713774|gb|AI943766.1|AI943766

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|60394503|gb|DN227373.1|DN227373

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|87156235|gb|DY401024.1|DY401024

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|71318153|gb|DR795840.1|DR795840

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|40302995|gb|CK347382.1|CK347382

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCTAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|60399673|gb|DN232483.1|DN232483

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|32846493|gb|CD986174.1|CD986174

EST:     ACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: ACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|6828042|gb|AW331685.1|AW331685

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|74232019|gb|DT639933.1|DT639933

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|5895801|gb|AW037047.1|AW037047

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|33942345|gb|CF348945.1|CF348945

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|4887302|gb|AI677401.1|AI677401

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|47961685|gb|CN844394.1|CN844394

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|21987487|gb|BQ779015.1|BQ779015

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|60357188|gb|DN224161.1|DN224161

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|20301592|gb|BQ164535.1|BQ164535

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|74232018|gb|DT639932.1|DT639932

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|78103532|gb|DV521960.1|DV521960

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|76917636|gb|DV166930.1|DV166930

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|113795218|gb|DW911359.1|DW911359

EST:     GGCTTGCTTGCTTTGAGAGAGCGGTGGATGAAG                         GTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: GGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|78023275|gb|DV491662.1|DV491662

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|5650117|gb|AI920477.1|AI920477

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|78544201|gb|DV621699.1|DV621699

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|67015613|gb|CO444362.1|CO444362

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

EST: gi|6022662|gb|AW067474.1|AW067474

EST:     CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAG                         GTGACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG
genomic: CCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAG

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187

AGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagc ... gttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTCATCAGCAGCGC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 332

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 229

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aggtcacagaaaatatccactcatgaactgctatttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTCATCAGCAGCGC

                                 tttttattttctgtt  CT-rich tract
                               tatttttattttctgt  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

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attcaccagagttaaccttttgtaatagcctgcaacttgaatacaaggtcacagaaaatatccactcatgaactgctatttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTCATCAGCAGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- -caccaga
- - - - - - - - - - - - - -gcctgca
- - - - - - - - - - - - - - - - - - - -aatacaa
- - - - - - - - - - - - - - - - - - - - - - - - - acagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaac