Sequence
atgc intronic sequence ATGC exonic sequence...gttggtgtcttggtggtaccatgtcagttgtcaacagtccaatttcattctcatggctttgattctgacgtatgattatgtttattttaaatttgtgcagATTCTTTCAAGGCAATCAACGATGAAGGCATGCCCATGTATCAGAGGCCCTTCATGAAGGGCAAGCTGTACATCCACTTCTCGGTGGAGTTCCCGGACTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G056988_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G38790.3 (Glycine max), 3'ss of exon 5
-gttggtgtcttggtggtac-catgtcagttgtcaacagtccaatttcattctcatggctttgattctgacgtatgattatgtttattttaaatttg---tgcagATTCTTTCAAGGCAATCAACGATGAAGGCATGCCCATGTATCAGAGGCCCTTCATGAAGGGCAAGCTGTACATCCACTTCTCGGTGGAGTTCCCGGACTC
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gcctggtatgtaaatgattcacatatggcttagtcactgtgttacttt-tgcttgttgattgaattgaaacttg-aatcttattaacttttaatgttacttgcagAGTCATTCAAGGCAATAAATGATGAGGGAATGCCAAACTACCAGAGGCACTTCCTGAAGGGAAAGCTTTACATTCATTTCTCAGTGGAATTTCCTGATAC
upper sequence: GRMZM2G056988_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G38790.1 (Glycine max), 3'ss of exon 5
gttggtgtcttggtggtac-catgtcagttgtcaacagtccaatttcattctcatggctttgattctgacgtatgattatgtttattttaaatttg---tgcagATTCTTTCAAGGCAATCAACGATGAAGGCATGCCCATGTATCAGAGGCCCTTCATGAAGGGCAAGCTGTACATCCACTTCTCGGTGGAGTTCCCGGACTC
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----gtatgtaaatgattcacatatggcttagtcactgtgttacttt-tgcttgttgattgaattgaaacttg-aatcttattaacttttaatgttacttgcagAGTCATTCAAGGCAATAAATGATGAGGGAATGCCAAACTACCAGAGGCACTTCCTGAAGGGAAAGCTTTACATTCATTTCTCAGTGGAATTTCCTGATAC
upper sequence: GRMZM2G056988_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G10150.1 (Glycine max), 3'ss of exon 5
gttggtgtcttggtggtaccatgtcagttgtcaacagtccaatttcattctcatggc--tttgattctgacgtatgattatgtttattttaaatttgt-------gcagATTCTTTCAAGGCAATCAACGATGAAGGCATGCCCATGTATCAGAGGCCCTTCATGAAGGGCAAGCTGTACATCCACTTCTCGGTGGAGTTCCCGGACTC
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----gtatgtaaatgat-tcacgcctgcc-ccagttttgctgtgtgattaaattggtaatttcattatgtgctaagaaaattccaactttttgctggttatacatgcagATTCATACAAGGCTATAAATGATGAGGGAATGCCCATGTATCAGAGGCCATTCATGAAGGGGAAACTTTACATTCACTTCACTGTGGAGTTTCCAGATTC
upper sequence: GRMZM2G056988_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G17930.3 (Glycine max), 3'ss of exon 5
-gttggtgtcttggtggtaccatgtcagttgtcaacagtccaatttcattctcatggct--ttgattctgacgtatgattatgtttattttaa-----atttgtgcagATTCTTTCAAGGCAATCAACGATGAAGGCATGCCCATGTATCAGAGGCCCTTCATGAAGGGCAAGCTGTACATCCACTTCTCGGTGGAGTTCCCGGACTC
|||| | | || | | || || | | | | | ||| ||| | || ||| || | || || | | ||| || ||||||||| | |||||| || || ||||| || |||||||||||||||||| | ||||||||||| ||||| ||||| |||||| | ||||||||||| || ||
gcctggtatgtaaatgattca----cacctgccccaattttgctgtgattaaattggttattttattatgtgccaagaaaattctaactttgctggttatacatgcagATTCATACAAGGCTATAAATGATGAGGGAATGCCCATGTATCAGAGGTCATTCATGAAGGGGAAGCTTTACATTCACTTCACTGTGGAGTTCCCAGATTC
upper sequence: GRMZM2G056988_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G38790.2 (Glycine max), 3'ss of exon 5
gttggtgtcttggtggtac-catgtcagttgtcaacagtccaatttcattctcatggctttgattctgacgtatgattatgtttattttaaatttg---tgcagATTCTTTCAAGGCAATCAACGATGAAGGCATGCCCATGTATCAGAGGCCCTTCATGAAGGGCAAGCTGTACATCCACTTCTCGGTGGAGTTCCCGGACTC--
|| | | || | | ||| | || || || | || | || | | || ||| || | || | || | ||| ||| | |||||| || ||||||||||| || ||||| || ||||| | || ||||||| |||| ||||||| ||||| ||||| || ||||| ||||| || || || |
----gtatgtaaatgattcacatatggcttagtcactgtgttacttt-tgcttgttgattgaattgaaacttg-aatcttattaacttttaatgttacttgcagagTCATTCAAGGCAATAAATGATGAGGGAATGCCAAACTACCAGAGGCACTTCCTGAAGGGAAAGCTTTACATTCATTTCTCAGTGGAATTTCCTGATACCC
upper sequence: GRMZM2G056988_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G17930.1 (Glycine max), 3'ss of exon 5
gttggtgtcttggtggtacc-atgtcagttgtcaacagtccaatttcattctcatggctttgattctgacgtatgattatgtttattttaaatttgtgcagATTCTTTCAAGGCAATCAACGATGAAGGCATGCCCATGTATCAGAGGCCCTTCATGAAGGGCAAGCTGTACATCCACTTCTCGGTGGAGTTCCCGGACTC
|| || | | ||| || || | | || || || | | || | | | | || ||| | || ||||||||| | |||||| || || ||||| || |||||||||||||||||| | ||||||||||| ||||| ||||| |||||| | ||||||||||| || ||
gtatgtaaatgattcacacctgccccaattttgctgtgattaaattggttatttta--ttatgtgccaagaaaattctaactttgctggttatacatgcagATTCATACAAGGCTATAAATGATGAGGGAATGCCCATGTATCAGAGGTCATTCATGAAGGGGAAGCTTTACATTCACTTCACTGTGGAGTTCCCAGATTC
upper sequence: GRMZM2G056988_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0073g00560.t01 (Vitis vinifera), 3'ss of exon 6
gttggtgtcttggtggtaccatgtcagttgtcaacagtccaatttcattctcatggctttgattctgacgtatgattatgtttattt-taaatttgtgcagATTCTTTCAAGGCAATCAACGATGAAGGCATGCCCATGTATCAGAGGCCCTTCATGAAGGGCAAGCTGTACATCCACTTCTCGGTGGAGTTCCCGGACTC
| | | | | | | | | | | | || || |||| | | | | | || | | | | | |||| |||||||| || || |||||||| |||||||| || |||| ||| ||||||||||| || ||||||| ||||| | ||||| ||||| |||||
-gcgatactgtaagagaataaaaatattctcctgaaatttcagctctgggctttgactttctgttttcttggttgtgacccttgtctatgtttccatacagACCAATTCAAGGCTATAAATGATGAAGGAATGCCCATTTACCAGAAGCCATTCATGAAGGGGAAATTGTACATTCACTTTGCAGTGGATTTCCCTGACTC
upper sequence: GRMZM2G056988_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0080g01230.t01 (Vitis vinifera), 3'ss of exon 5
gttggtgtcttggtggtaccatgtcagttgtcaacagtccaatttcattctcatggctttg--attctgacgtatgattatgtttattttaa--atttgtgcagATTCTTTCAAGGCAATCAACGATGAAGGCATGCCCATGTATCAGAGGCCCTTCATGAAGGGCAAGCTGTACATCCACTTCTCGGTGGAGTTCCCGGACTC
||| || | | | |||| || ||| | | | || || | ||| | || | | | | || ||||||| |||||||||||||| || || || ||||| || || |||||||| ||||||| ||| ||||| |||||||| ||| ||||||||||||||| |
gttagtaatgtcatatctctatgtttcttttcatta-catggctctctctgtgtgatttggtcatttaaatgttgactggggggtgggggagttgttaatgcagATCAGTTCAAGGCAATCAATGACGAGGGAATGCCAATATACCAGAGGCCATTCATGAGGGGGAAGCTATACATCCAGTTCAACGTGGAGTTCCCGGACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattctcatggctttgattctgacgtatgattatgtttattttaaatttgtgcagATTCTTTCAAGGCAATCAACGATGAAGGCATGCCCATGTATCAGAGGCCCTTCATGAAGGGCAAGCTGTACATCCACTTCTCGGTGGAGTTCCCGGACTC
ttctgac putative branch site (score: 2)
tatgattatgtttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtgtcttggtggtaccatgtcagttgtcaacagtccaatttcattctcatggctttgattctgacgtatgattatgtttattttaaatttgtgcagATTCTTTCAAGGCAATCAACGATGAAGGCATGCCCATGTATCAGAGGCCCTTCATGAAGGGCAAGCTGTACATCCACTTCTCGGTGGAGTTCCCGGACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG