Sequence
atgc intronic sequence ATGC exonic sequencegtattccccttttctcccaattaattgtactatatccattgtactgatgagcagcagtattaggttggtgttggtctaatgcttgatatttttaaaatataaccagactaaattctgatgtctgtgacttagGATGAAGTTATTCAAAGGGAAGAAGCAATAAGAAAAGAGTATAAAGAACTTGACACAGTCTGGTTTATGGCAGGTTCTCTATTTCAG
Basic information
species | Glycine max |
transcript | GLYMA05G07100.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G07100.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G047695_T01 (Zea mays), 3'ss of exon 3
gtattccccttttctcccaattaattgtactatatccattgtactgatg-agcagcagtattaggttggtgttggtctaatgcttgatattttt--aaaatataaccagactaaatt--ctgatgtctgtgacttagGATGAAGTTATTCAAAGGGAAGAAGCAATAAGAAAAGAGTATAAAGAACTTGACACAGTCTGGTTTATGGCAGGTTCTCTATTTCAG
| || | | | | ||| | || | || | | | ||| | ||| | | | |||||| | | || || | | |||| | ||||| | | || ||||||||||| || || || || |||||||| | ||||||||| || ||||||||| | ||||||||||||||||| |||||||||
-----------gttagtggttttactatgttgcatctcaattctcaatataacattattgcttt-ttgatattgaaggattacacgatattctgtaagaacattaatatcctaacatagctgatatatttg---cagGATGAAGTTGTTGCTAGAGATGAGGCAATAAGGAGAGAGTATAATGAGCTTGACACATTGTGGTTTATGGCAGGTTCACTATTTCAG
upper sequence: GLYMA05G07100.1 (Glycine max), 3'ss of exon 3
lower sequence: AC198982.3_FGT006 (Zea mays), 3'ss of exon 1
gtattccccttttctcccaattaattgtactatatccattgtactgatg-agcagcagtattaggttggtgttggtctaatgcttgatatttttaaaatataaccaga-ctaaattctgatgtctgtgact-tagGATGAAGTTATTCAAAGGGAAGAAGCAATAAGAAAAGAGTATAAAGAACTTGACACAGTCTGGTTTATGGCAGGTTCTCTATTTCAG
| || | | | | |||| | ||| | || | | | ||| |||| | | | ||||| | ||| | | | | | | || | |||| | || | ||||||||||| || || || || |||||||| | ||||||||| || ||||||||| | ||||||||||||||||| |||||||||
-----------gttagtggttttactcttttgtatctcaattctcaatgtaacattattgccat-ttgacgttgcaggattattcaatattctgcaaaaacatcaatatcctaacttagatga-tatgtttgcagGATGAAGTTGTTGCTAGAGATGAGGCAATAAGGAGAGAGTATAATGAGCTTGACACATTGTGGTTTATGGCAGGTTCACTATTTCAG
upper sequence: GLYMA05G07100.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S181_117V6.1 (Physcomitrella patens), 3'ss of exon 3
gtattccccttttctcccaattaattgtactatatccattgtactgatgagcagcagtattaggttggtgttggtctaatgct-tgatatttttaaaatataaccagactaaattctgatgtctgtgacttagGATGAAGTTATTCAAAGGGAAGAAGCAATAAGAAAAGAGTATAAAGAACTTGACACAGTCTGGTTTATGGCAGGTTCTCTATTTCAG
| || || | || | | | || |||| | | || | |||||| | | ||| | | ||| | | || | |||| | ||| | | || | || || | | || || |||||||||||||||| ||||||||||| |||||| |||| ||
---------------------------cgatgactcaataaaaaggagatgacttaatctt--tccagtgtcagattttaactatcatatttct----tttaagtaagtgacattttctcttgaatggttcagGAGGTAGTGTTAGAGAGATTGGCAGGTATCAAACGGGAATACGAAGAACTTGACACAGTGTGGTTTATGGCGGGTTCTTTATTCAAG
upper sequence: GLYMA05G07100.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S55_141V6.1 (Physcomitrella patens), 3'ss of exon 3
gtattccccttttctcccaattaattgtactatatccattgtactgatgag-cagcagtattaggttggtgttggtctaatgcttgatatttttaaaatataaccagactaaattctgatgtctgtgacttagGATGAAGTTATTCAAAGGGAAGAAGCAATAAGAAAAGAGTATAAAGAACTTGACACAGTCTGGTTTATGGCAGGTTCTCTATTTCAG
|| | | ||| | | ||||| | | || | | || | | ||||| | || | | ||||| | | | || |||| | ||| | | ||| | | || | | || || |||| ||||||||||| ||||||||||| |||||| ||||| ||
------------------------------aattcaaagcaaattgagaggacctgagtatcgctctccttttcatgttatttcttttctttttgttac-caattatgtgatattctctcg--tataacgcagGAAGTTGTTTTAGAGAGGTTGGCGGGTATCAAACGGGAATACGAAGAGCTTGACACAGTTTGGTTTATGGCGGGTTCTTTATTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgcttgatatttttaaaatataaccagactaaattctgatgtctgtgacttagGATGAAGTTATTCAAAGGGAAGAAGCAATAAGAAAAGAGTATAAAGAACTTGACACAGTCTGGTTTATGGCAGGTTCTCTATTTCAG
atatttttaaaatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattccccttttctcccaattaattgtactatatccattgtactgatgagcagcagtattaggttggtgttggtctaatgcttgatatttttaaaatataaccagactaaattctgatgtctgtgacttagGATGAAGTTATTCAAAGGGAAGAAGCAATAAGAAAAGAGTATAAAGAACTTGACACAGTCTGGTTTATGGCAGGTTCTCTATTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC