Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaattcaaaacgtcagaagaatggtgatttcagtttattagttaatacgtttcatgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA

Basic information

species Zea mays
transcript GRMZM2G074687_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g14270.2 (Oryza sativa), 3'ss of exon 2
-------gttaattcaaaacg--tcagaagaatggtgatttcagtttattagttaat-acgtttcatgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA
       |  |  |||| ||   |||     |   | |     | || ||| | ||| |  |||| |||||||||||| |||||||| ||||||||||||||||| || |||||||| || ||||| |||||||||||||||||||| ||||||||||||||||||||||| ||
gtaaattggaagatcaatacacctcattcagacactaacagatgatttttactgaattatttttcttgttgcagGTATCCAAACCTCTGAGGACTACAGGTTCTACGCTATTTCAGCGGAGTACCCAGAATTCAGCAACAAGGATAAAACCCTGGTGCTGCAGTTCTCTGTAAA

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G28890.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------gttaattcaaaacgtcaga-agaatggtgatttcagtttattagttaatacgtt--tcatgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA
                                                 | | ||    |   |     | ||| |  |||    | | || | |   | |||  |     ||||||||||||||||   ||||| ||||| |||||||| ||||||||||| |||||||||||||||||||||| |||||| || ||  | || || ||||| ||
gtaaactaaattgctatgttgaatagtcgggtattatactattattgttgctcatgtttacttttgtttaaaattgatattaagatatgtttggttgaatgttgatatctctgcagGTATTCAAACCAGTGAGGATTACAGATTCTATGCTATTTCAGCTGAGTACCCTGAATTCAGCAACAAGGGTAAGACACTAGTCTTTCAATTTTCTGTTAA

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 2
------------------------------------------------gttaattcaaaacgtcagaagaatggtgatttcagtttattagttaatacgt-ttcatgt---tgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA
                                                ||| |||     | | | |   ||  | |  |  |||| ||  |   |   | || || |   ||||||||||||||||   ||||| ||||| ||||| || ||||||||| | ||||||||||||||||||||||||||||| || ||  | || || ||||| ||
gtaaactaaattgctatattgaacagtcttgtattatttcttgctcatgtttatttttggc-taaaattgatattaagatatgtttgtttttggctgaatgttgatatctatgcagGTATTCAAACCAGTGAGGATTACAGATTCTACGCTATTTCAGCTCAGTACCCTGAATTCAGCAACAAGGATAAGACACTAGTCTTCCAATTTTCTGTCAA

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G09210.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------gttaattcaaaacgtcagaagaatggtgatttcagtttattagttaatacgtt-------------tcatgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA
                   | ||||   | |      |   || ||  |   || || |  | |||| ||||             |  | | |||||||| || |||   || |||||||| ||||| |||||||||||||| | |||||||||||| |||||||| |||||| | ||  | || ||||| || ||
gtatgattcagccttcagagctaatcacagaatcattatttattgttttacaagcttgt--gctaatgcgttgttgcaattgccattgtctggcagGTATCCAGACCAGTGAAGACTACAGATTCTACGCCATTTCAGCTGAGTTCCCTGAATTCAGTAACAAGGACAAGACCTTAGTCTTCCAATTCTCAGTCAA

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 2
gttaattcaaaacgtcagaagaatggtgattt--cagtttattagttaatacgtttcatg------ttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA
||   ||  |         |  ||| |||||      || ||    | ||     | ||       |||||||||| |||||   |||||||||||| ||||| || || |||||||||| |||||| || |||||||||||||||||| | ||  | || |||||||| ||
gtatgtttcatgaccagtgatgatgttgattcactgattcatattctcatgtcaattataactctcttgcagGTATCCAAACTAGCGAGGACTACAGATTCTACGCTATATCAGCTGAATTCCCTGAGTTTAGCAACAAGGATAAGACCTTAGTCTTCCAATTCTCTGTCAA

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------------------------------------------------gttaattcaaaacgtcagaagaatggtga-----tttcagtttattagt-taatacgtttcatgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA
                                                                                  | |||  |   || |      |  | |     ||||||  || |  | |  |  |  ||  | | |||||||||| ||    || ||||| | ||||||||| || |||||||| | |||||||||||| ||||||||||||||  ||||  | ||||| ||||| ||
gtatgctatccatcattatactgtctgtacattaacaaagacgaaaagtgctttgagacctcttgcttctgtttaagggttctcatttcaggtgtgattttccttattaagagttttcagactacttatatggtttgaatctgggtccagGTATTCAGACTAGTGAAGACTATAAGTTCTATGCAATCTCAGCTGAGTTCCCTGAATTCAGTAACAAGGATAAGACTTTGGTTTTCCAGTTTTCTGTTAA

upper sequence: GRMZM2G074687_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------------gttaattcaaaacgtcagaagaatggtgatttcagtttattagttaatacgtttcatgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA
                                                        ||||||   |   | | | |    || | || | || | |  | |||     ||  | |  |||||| |||||    ||||||||||| |||||||| || |||||||| |||||||||||||||||||| ||||||||  | ||  | || ||  |||| ||
gtattattttcatacacattcttatacctatttggggcaatgtttcattctctttattaatttggactttgaaatgt---gtaacttgatttgact--tcaatgg---tctggatatagGTATCCAAACAAGTGAGGACTACAGATTCTATGCTATATCAGCTGAGTACCCTGAATTCAGCAACAAAGATAAGACATTAGTTTTCCAATTTACTGTTAA

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|116822064|gb|EC865430.1|EC865430
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|148963585|gb|EE014618.2|EE014618
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|148948737|gb|EC898659.2|EC898659
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|149008411|gb|EE040568.2|EE040568
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|58029459|gb|CX724886.1|CX724886
EST:     GGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: GGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|149014111|gb|EE043648.2|EE043648
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|31558809|gb|CD528021.1|CD528021
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|148935865|gb|EC879913.2|EC879913
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|149097674|gb|EE183578.2|EE183578
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|148959988|gb|EE153227.2|EE153227
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|149112807|gb|EE295617.2|EE295617
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|149011835|gb|EE042440.2|EE042440
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|148996195|gb|EE035467.2|EE035467
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAANTAC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAA-TAC
EST: gi|149084306|gb|EE173743.2|EE173743
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
EST: gi|148935504|gb|EC879545.2|EC879545
EST:     TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAG                         GTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC
genomic: TGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACC

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: 34 (upstream exon), 42 (downstream exon)
Score: 75

GAAAGTCGGTGGGTCAAGTCCGAGTGGAAAAAGGACGATAACATGGCTGGTGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 131

GAAAGTCGGTGGGTCAAGTCCGAGTGGAAAAAGGACGATAACATGGCTGGTGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 115

GAAAGTCGGTGGGTCAAGTCCGAGTGGAAAAAGGACGATAACATGGCTGGTGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 819

GAAAGTCGGTGGGTCAAGTCCGAGTGGAAAAAGGACGATAACATGGCTGGTGAATGGAACCACACCTCGGGGAAATGGAATGGAGATGCAGAGGACAAAGgttaattcaa ... catgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacgtcagaagaatggtgatttcagtttattagttaatacgtttcatgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA
                                agttaat  putative branch site (score: 819)
                   atttcagtttattagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaattcaaaacgtcagaagaatggtgatttcagtttattagttaatacgtttcatgttgcagGTATTCAAACCTCCGAGGACTACAGGTTCTATGCCATTTCAGCTGAATACCCTGAATTCAGCAACAAGGATAAGACCCTGGTGCTGCAGTTCTCTGTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG