Sequence
atgc intronic sequence ATGC exonic sequencegttggttgttctcacttctcattagcatatatattcttgggaaacttttgccctttatcttttatttttaattgaagagtagtagattttgataattttctttctgaattgactttggtgctatgcctccagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
Basic information
species | Glycine max |
transcript | GLYMA08G13070.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G138349_T02 (Zea mays), 3'ss of exon 6
gttggttgttctcacttctcattagcatatatattcttgggaaacttttgccctttatcttttatttttaattgaagagtagtagattttgataattttctttctgaattgactttggtgctatgcctccagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG----
| || ||| | | ||| | || | | || || | || | |||| || | || | | || | || || | |||| | || || | ||||| || | || ||||||| ||||||||||| ||||| | ||| |||||||| ||||||| |||| |||| ||
----------------------------------------gtaattttggtcgttt-tgttagaatcacaacaaaataaacatatactttgtta-tcaaattacagcgcc--ctcttgt----tgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTGGTAA
upper sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G138349_T04 (Zea mays), 3'ss of exon 3
gttggttgttctcacttctcattagcatatatattcttgggaaacttttgccctttatcttttatttttaattgaagagtagtagattttgataattttctttctgaattgactttggtgctatgcctccagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
| || ||| | | ||| | || | | || || | || | |||| || | || | | || | || || | |||| | || || | ||||| || | || ||||||| ||||||||||| ||||| | ||| |||||||| ||||||| |||| |||| ||
----------------------------------------gtaattttggtcgttt-tgttagaatcacaacaaaataaacatatactttgtta-tcaaattacagcgcc--ctcttgt----tgattgcagAAAGCACAAACTTCAGTAATCAATGGCAACCTGAATCCTGTCTGGAATGAAGAACTGAAGCTCTCTGTTCCCCAGCAATATGGACCTCTGAAGCTG
upper sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 6
gttggttgttctcacttctcattagcatatatattcttgggaaacttttgccctttatcttttatttttaattgaagagtagtagattttgataattttctttctgaattgactttggtgctatgcctccagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
| || | | | | | | | |||| ||| | |||||| | || || | | ||| | | ||| | | | ||||||| | || | ||||| | ||| | |||||| | ||||| || || || || ||||||||||||||||| ||||| ||||||||||| | | ||| | |||| |||
-----------gtaattatagtgaatacttttgaaatcttgaaaggttttctctttatatgttcttaccattgtttaagtgatcattattgtcatctctttttctgat----cgttatcatcgttttaccagAAGGCTCAATCTACTGTAGTGAAGAGCAACTTAAACCCTGTCTGGAATGAGGAACTCATGCTCTCTGTTCCTCATAACTATGGCTCAGTGAAATTG
upper sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 7
gttggttgttctcacttctcattagcatatatattcttgggaaacttttgccctttatcttttatttttaattgaagagtagtagattttgataattttctttctgaattgactttggtgctatgcctccagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
| | ||||| | |||||| || ||| | || | | ||||| | | | ||| | | || || | | | |||| ||||||||||||| || || ||||||||||| || || |||||| | ||||| ||||||||||||||| || | ||| |||| |||
--------------------------------------gtaagtgatttgctttgcatcttt--ttattagct-----ttacttcttgttgatgctgtgaatcttgagtaaaatt--gtcttgtttattcagAAACTTCAGACAACTGTTATGAATAGTAATTTGAACCCGGTATGGAATCAAGAACTCATGCTGTCTGTTCCTGAGAGCTATGGCCCTGTGAAATTG
upper sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 7
gttggttgttctcacttctcattagcatatatattcttgggaaacttttgccctttatctt---ttatttttaattgaagagtagtagattttgataattttctttctgaattgactttggtgctatgcctccagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
|| ||| | | |||| | | | || ||||| || | ||| | | || | | | | |||| || | | || | ||||||| |||||| ||||||| ||| || |||||||||||||||||||||||||| ||||| ||||| || | | | ||| | || ||
-----------------------------cattgtctagattagattttagtcaaagtggtgaattgcttttagttagacagtgatcattctt--ttactgataatgaagattggctgttgc----tgttactagACTGTCCAGACACAGGTAATAACGAGCAACTTGAATCCAGTCTGGAATGAGGAACTCATGCTTTCTGTGCCCATGGATTATGGGCCCATAAAAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtagtagattttgataattttctttctgaattgactttggtgctatgcctccagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
aattgac putative branch site (score: 3)
tgcctcc putative PPT
tagattttgataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggttgttctcacttctcattagcatatatattcttgggaaacttttgccctttatcttttatttttaattgaagagtagtagattttgataattttctttctgaattgactttggtgctatgcctccagACTGTTCAGACAACTGTAATAAAGAGTAATTTGAATCCAGTCTGGAATGAGGAACTTATGCTGTCTGTTCCTCAGCAATTTGGAATATTGAATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG