Sequence
atgc intronic sequence ATGC exonic sequencegtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
Basic information
species | Glycine max |
transcript | GLYMA11G06720.1 |
intron # | 26 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
gtgaatcttacttatcttttgtcttattttgacaattag-caaaaatcgagatcag-aatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
| | ||||| | | | | | ||||||| ||| | ||| ||| | | | | | | ||| | | ||| ||| |||||||||||||| | |||||||||||| | | |||||||||||||||||||| || || |||||||||||||| ||||| |||| ||||||||||
--------------------------gtaaagcgattagatgattgtactgcttattgatgttatttttccttt----tttttttattttgaataactaatggctggaatgc-cttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
| | || | | ||| | ||| | || | | | | | |||| ||||||| | || || ||| ||| | | ||| ||| |||||||||||||| | |||||||||||| | | |||||||||||||||||||| || || |||||||||||||| ||||| |||| ||||||||||
---------gtaaagcgattatatgattgtactgctta-------ttgatgttatttttccttttttattttat----tttgaataactaatggctgg-------aatgc-cttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatg-ttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
| | || || || | | | | || || ||| | || || || ||| || || | ||||||| | |||||||||||| | |||||||||||| | |||||||||||||||||||||| || || || |||||||||||||||||| | ||||||||||| |
----------------gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcattt-cttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 3
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
|| | || | | |||| || | ||| || | | ||| || || || | || || | ||| | | | | | |||||| |||||||||||||| | || ||||||||| | |||||||||||||||||||||| || || || |||||||||||||||||| | ||||||||||| |
gtacaaaatagccagata--atcttgcagtgcctatt-gctgctgctgttgttgtaat--cgtgcgatgcatattgttactgctttttaatttaataacctgtgtccatttctggagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 11
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
| || || || || || |||| || || | || | || || || | ||| | ||||||| |||||||||||||| | || ||||||||| | | || ||||||||||||||||| || || || |||||||| ||||||||| | || ||||||||||
------------------------------gtaaaataaaaataaaatag-ccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgttaatttat-tgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCCATTGCTCTATCGAAGAAAGACA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 6
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
| || || || || || |||| || || | || | || || || | ||| | ||||||| |||||||||||||| | || ||||||||| | | || ||||||||||||||||| || || || |||||||| || |||||| | || ||||||||||
------------------------------gtaaaataaaaataaaatag-ccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgttaatttat-tgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 25
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
| || || || || || |||| || || | | | || || || | | ||| | ||||||| |||||||||||||| | || ||||||||| | | || ||||||||||||||||| || || || |||||||| || |||||| | || ||||||||||
------------------------------gtaaaataaaaataaaatag-ccagacagtcgtgcaattcctgtcgctaccgcttttaatttaatagcatgtgttaatttat-tgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 11
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
| || || || || || |||| || || | || | || || || | ||| | ||||||| || ||||||||||| | || ||||||||| | | || ||||||||||||||||| || | || |||||||| || |||||| | || ||||||||||
------------------------------gtaaaataaaaataaaatag-ccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgttaatttat-tgagcagCTTCAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGACAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 26
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattat-tattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
| | | || || | | ||||| | | || | | | | | || | | | || | || ||| ||||||| ||||| ||||| |||||||||||| ||||||| || ||||| ||||||||||| |||||||| ||||||||||| ||||||||||||||||
-----------------------------------gtgagagagattgaatttattttgttaatgttggtaggcttcataagcagaacatgtacataagatctagtgatgcgtgtggacagGTTGAGAAACATGAGCTTCTGGAGATGAGGCGTATTGCTGCTTATATTTATAAGAAAGCAGGTAGATGGAAACAATCCATTGCATTGTCAAAGAAAGACA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 14
---------gtgaatcttacttatc--ttttgtcttattttgacaattagcaaaaatcgagatcaga--atgttatgggaaatttaaaatatttgaattat---tatt----gattggcttcaaca----atacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
|| || || ||| ||| | ||| | || | | || || | |||| || | | ||| | ||| || | |||| | || ||| ||| | |||||||||||||| |||||||| || ||| | || |||| ||| ||||| || |||| ||| || |||||||| ||||| | |||||||| ||||||||||
gtaagttccgtagtcattgctaatcagtttaatactatcaatatcatccatatgtgtttttattagttcacaacatggaaagtgtcaaagttgtgacttttatgtatttcccaggtaaatttgacatgttatatttttttacagATTGAGAAGCACGAACTTCTGGAAATGCGTCGCGTTGGTGCGTACATCTATAAGAGAGCTGGCAGATGGAAACAATCTGTGGCTTTGTCCAAGAAAGACA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 26
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
||| ||| || ||| || | || || | | | | || | |||| |||| ||||| || ||| | || || | || || |||||||||||||||||||||||||||||||| || || |||| |||| ||||| ||||
----------------------------------------------------------gtttgaggatccttgc----tttttcttgtgatcttttaacatggaagacactgttttgcagCTTGAAAAGCACGAGCTTATCGAATTGCGCCGCGTCTCTGCCTACATTTACAAGAAAGCAGGAAGATGGCGCCAGTCTGTTGCGCTGTCCAAGAAGGACA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 26
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
||| ||| || ||| || || || | | | | || | |||| |||| ||||| || ||| | || || | || || |||||||||||||||||||||||||||||||| || || |||| |||| ||||| ||||
----------------------------------------------------------gtttgaggatccttgc----tttttcttgagatcttttaacatggaagacactgttttgcagCTTGAAAAGCACGAGCTTATCGAATTGCGCCGCGTCTCTGCCTACATTTACAAGAAAGCAGGAAGATGGCGCCAGTCTGTTGCGCTGTCCAAGAAGGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
tattgat putative branch site (score: 3)
ttaaaatatttgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA