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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtactgctaacttgtgtgtagccagctttggttcctacttcataattaatgacaacacttagttttgtttatgagataacaccgaattgagccatgtttacttattgccattacgtatcactatatcactaacaattaacaagtaaaccttgtttactgcaatgatttgcatgtgacattgtgcagGAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTGAAGAGACTCATCTATACTAGTTCACCTAGTGTCGTGTTTGATGGAGTTCATGGAATTTT

Basic information

species Zea mays
transcript GRMZM2G149224_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149224_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g29170.2 (Oryza sativa), 3'ss of exon 2
gttggtactgctaacttgtgtgtagccagctttggttcctacttcataattaatgacaacacttagttttgtttatgagataacaccgaattgagccatgtttacttattgccattacgtatcactatat-cactaaca-attaaca-agtaaaccttgtttactgcaatgatttgcatgtgacattgtgcagGAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTGAAGAGACTCATCTATACTAGTTCACCTAGTGTCGTGTTTGATGGAGTTCATGGAATTTT
                                                                                           | ||  |  || | ||      |||   | | |  || | || | | | | ||    | ||||  |||| || ||  | || ||| |     ||||   |||||||||||||||| |||||| |||| ||||||||||||||||||||||| ||||| || |||||||| ||||| || || |||||| |||||||||| ||
-------------------------------------------------------------------------------------------ttagtaacattaattttggattattttttctaatcattttcaatgatatagtactgcattaaagtttgtcta-tgtga-gacttgtacaatgcatttcacagGAACAAAGAATGTCATTGACGCTTGCATCCGTTGCAAGGTGAAGAGACTTATCTACACCAGTTCACCAAGTGTAGTTTTCGATGGAATTCATGGAATCTT
















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|149072461|gb|EE160738.2|EE160738
EST:     AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATG                         GAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTGAAGAGACTCA
genomic: AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATGgttggtactg ... cattgtgcagGAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTGAAGAGACTCA
EST: gi|211071352|gb|FL056275.1|FL056275
EST:     AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATG                         GAACAAAGAATG
genomic: AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATGgttggtactg ... cattgtgcagGAACAAAGAATG
EST: gi|211071355|gb|FL056278.1|FL056278
EST:     AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATG                         GAACAAAGAATGT
genomic: AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATGgttggtactg ... cattgtgcagGAACAAAGAATGT
EST: gi|211074087|gb|FL056287.1|FL056287
EST:     AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATG                         GAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTG
genomic: AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATGgttggtactg ... cattgtgcagGAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTG
EST: gi|211074092|gb|FL056292.1|FL056292
EST:     AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATG                         GAACAAAGAATGTTATTGACGCTTGTAT
genomic: AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATGgttggtactg ... cattgtgcagGAACAAAGAATGTTATTGACACTTGTAT
EST: gi|211074086|gb|FL056286.1|FL056286
EST:     AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATG                         GAACAAAGAATGTTATTGACGCTTGTATCCGTTGGCA-GGTGAAGAGACTC
genomic: AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATGgttggtactg ... cattgtgcagGAACAAAGAATGTTATTGACACTTGTATCCGTTG-CAAGGTGAAGAGACTC
EST: gi|211071356|gb|FL056279.1|FL056279
EST:     AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATG                         GAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTGAAGAGACTCA
genomic: AGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATGgttggtactg ... cattgtgcagGAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTGAAGAGACTCA

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: 105

CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATGgttggtactg ... cattgtgcagGAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTGAAGAGACTCATCTATACTAGTTCACCTAGTGTCGTGTTTGATGGAGTTCATGGAATTTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 56

CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATGgttggtactg ... cattgtgcagGAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTGAAGAGACTCATCTATACTAGTTCACCTAGTGTCGTGTTTGATGGAGTTCATGGAATTTT


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 42

CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATGgttggtactg ... cattgtgcagGAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTGAAGAGACTCATCTATACTAGTTCACCTAGTGTCGTGTTTGATGGAGTTCATGGAATTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATGgttggtactg ... cattgtgcagGAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTGAAGAGACTCATCTATACTAGTTCACCTAGTGTCGTGTTTGATGGAGTTCATGGAATTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaattaacaagtaaaccttgtttactgcaatgatttgcatgtgacattgtgcagGAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTGAAGAGACTCATCTATACTAGTTCACCTAGTGTCGTGTTTGATGGAGTTCATGGAATTTT
                             aatgattt  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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtactgctaacttgtgtgtagccagctttggttcctacttcataattaatgacaacacttagttttgtttatgagataacaccgaattgagccatgtttacttattgccattacgtatcactatatcactaacaattaacaagtaaaccttgtttactgcaatgatttgcatgtgacattgtgcagGAACAAAGAATGTTATTGACACTTGTATCCGTTGCAAGGTGAAGAGACTCATCTATACTAGTTCACCTAGTGTCGTGTTTGATGGAGTTCATGGAATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA