Sequence
atgc intronic sequence ATGC exonic sequence...tatgttaaatttcttttaaaggtatactcgataaaattaactgtcttacattcacatatttttatgccaatgatatcccctgtcttgcaacaatgtttagGCAGTCCTGTTCTTGGCTACTTGGCTGCCGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
Basic information
species | Glycine max |
transcript | GLYMA09G39770.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 3
-tatgttaaatttcttttaaaggtatactcgataaaattaactgtcttacattcacatatttttatgccaatgatatcccctgtcttgcaacaatgt-ttagGCAGTCCTGTTCTTGGCTACTTGGCTGCCGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
| || | || | | || ||| || | | || ||| | | ||| | | || | | || | || | |||||||||||||||||||| || | ||||| ||| || | ||||| || ||||| ||||| ||||| ||| | || ||||||||||| ||| | || |||||
atgtgcatacaaaagttgagaaacatctgtgattaagatcatcagttttcatggaagtttttgtgaccttctgcaaataa--attttaccttgatatcttagGCAGTCCTGTTCTTGGATATCTTGCTGCTGGTGTCCTCATTGGTCCATATGGGCTCTCCATCATCCGTAATGTGCATGGGACAAAGGCAATTGCGGAATT
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------------------tatgttaaatttcttttaa-aggtatactcgataaaattaactgtc-------ttacattcacatatttttatgccaatgatatcccctgtcttgcaacaatgtttagGCAGTCCTGTTCTTGGCTACTTGGCTGCCGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
|| | ||| | | | || | || | | | || | | | | | |||| |||| | | | | ||| |||| | ||||||| ||||||||||| || ||||| || || ||||||||||| |||||||||||||| || |||||| | || ||||| || || || | || |||||
gtaacgtaatatattaattcactcattgtattttaaatccccatattttgtcctccttgtttcatttggacttgtactattcattgttatcatcagacaaaccatttcacttctgttgccgcaatcataatgcatagagatttaaatgctatcttgttggtttcttctgctgcaatctatagGCAGCCCTGTTCTTGGGTATTTGGCGGCGGGAATCTTGATTGGTCCTTATGGTCTCTCAATAATTCGTAATGTGCATGGAACCAAGGCCATTGCAGAATT
upper sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 2
-tatgttaaatttcttttaaaggtatactcgat-aaaattaactgtcttacattcacatatttttatgccaatgatatcccctgtcttgcaacaatgtttagGCAGTCCTGTTCTTGGCTACTTGGCTGCCGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
|| | | | | | || | | ||| || | || | | | ||| || | | || | ||| || || ||||||||||||||||||||||| ||||||||||| |||||||||||||||||||||||||||||||| |||||||| || |||||||| ||||| | || |||||
gcatatatatgtcactgtgccttcatttcctttcaaagtttattgccaagtttctgtactgtttcattgatagtgtgtcttccatct-gctgca-tgtttagGCAGTCCTGTTCTTGGTTACTTGGCTGCTGGTATCTTGATTGGGCCTTATGGTCTCTCTATTATTCGTCATGTACATGGGACCAAAGCGATTGCAGAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacattcacatatttttatgccaatgatatcccctgtcttgcaacaatgtttagGCAGTCCTGTTCTTGGCTACTTGGCTGCCGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
gtcttac putative branch site (score: 3)
ttcacatatttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgttaaatttcttttaaaggtatactcgataaaattaactgtcttacattcacatatttttatgccaatgatatcccctgtcttgcaacaatgtttagGCAGTCCTGTTCTTGGCTACTTGGCTGCCGGTATCTTGATTGGGCCTTATGGTCTCTCTATCATTCGTCACGTTCATGGGACAAAAGCAGTAGCTGAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - aaaattaa
- - - - - - - - - - - - - - - - - - - - ctgtctt
- - - - - - - - - - - - - - - - - - - - - - - - cattcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcca