Sequence
atgc intronic sequence ATGC exonic sequence...ttgcatttcctttatgcaatatattttgttggaaaaatggtgtttagcataaacaattttgattttgatggatttgttattatgttttcatcgatgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTCTTGAAGGTCCATGGTCCCAGAACAATCTTGATAATGGGG
Basic information
species | Glycine max |
transcript | GLYMA05G30530.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 8
------ttgcatttcctttatgcaatatattttgttggaaaaatggtgtttagcataa--acaattt----tgattt-tgatggat----ttgttattatg-ttttcatcg----------atgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTCTTGAAGGTCCATGGTCCCAGAACAATCTTGATAATGGGG
|| || ||| || ||| | |||| | ||| | | || | || || ||| ||| || |||| | | ||||| |||| ||| |||| | |||||||||||||||| | |||||||| || ||||| |||||||||||||| ||||||||| |||| ||||| ||||||||||| ||| | |||||||| |
gtttgtttacacttc-ttgatgacctcacctttgctagaagagttttgaacaattgaactgcattttgttatgacttgtgatagttgtttttgtttatatgatttgcatcttatgctctacacttcagGATAATAAAGATGTGAGGCATGTTAAGACTTATGAAGTTGCACTGAAGGACAAAGATTTTGTTGAGGGTCCTTGGTCCCAGAATAATGTAGATAATGGTG
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 8
ttgcatttcctttatgcaatatattttgttggaaaaatggtgtttagcataaacaattttgattttgatggatttgttattatgttttcatcgatgac--agGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTCTTGAAGGTCCATGGTCCCAGAACAATCTTGATAATGGGG
| ||| | | ||| ||| ||| || | | | || | | |||| | || || | | | | || | |||| | | |||| || ||||||||||||||||| ||||||||||| || | || || ||||| |||||| | || ||||||||||| ||||||| ||| || ||||| |
-ttttttttaactttataatctatattgatgatgtagtctgttgtacgagatgcaatctagaggtttctccggt-gggactaactaatcattggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGATAAGGATTTTGTCGAGGGTCCATGGTCTCAGAACAGTCTCGACAATGGTG
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 8
---ttgcatttcctttatgcaatatattttgttggaaaaatggtgtttagcataaacaattttgattttgatggatttgttattatgttttcatcgatgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTCTTGAAGGTCCATGGTCCCAGAACAATCTTGATAATGGGG
|| |||| | || | | ||| ||| | | | | | ||| || |||| ||| | || | | | | | |||||| || ||||||||||||||||| ||||||||||| ||| | || |||||||| | ||| | |||||||||||||| ||||||||||| || ||||| |
ctgctgtattttttaaataaattgtatcttggtttactttgctaatgcaatgtgctcaaggatg--tttgctgggtgaactaattaatgcttgg-gtttacagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTTTCTCTAAAGGATAAGAACTTTGTCGAAGGTCCATGGTCACAGAACAATCTCGACAATGGTG
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 8
---ttgcatttcctttatgcaatatattttgttggaaaaatggtgtttagcataaacaattttgattttgatggatttgttattatgttttcatc--gatgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTCTTGAAGGTCCATGGTCCCAGAACAATCTTGATAATGGGG
|| || || || | ||| ||| | | | ||| ||| | || | | | ||||| | || | | || || || |||||||| |||||||| ||||||||||||||||||||||| || |||||||||| |||||| |||| ||||| ||| | ||||||||||| || |||||||
aacttagatggccccactgtgttccattatgtagcatcagaagtg-----cattaggaagaataactcagatggcctcaccatgttctcttgattcaaattgcagGATAACAAAGATGCACGTCATGTTAAAACATATGAGGTGGCTTTGAAGGATAAGGATTTTGTTGAGGGTCCTTGGGCTCAGAACAATCTAGACAATGGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcataaacaattttgattttgatggatttgttattatgttttcatcgatgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTCTTGAAGGTCCATGGTCCCAGAACAATCTTGATAATGGGG
ttttgat putative branch site (score: 4)
ttttcatc putative PPT
atttgttattatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcatttcctttatgcaatatattttgttggaaaaatggtgtttagcataaacaattttgattttgatggatttgttattatgttttcatcgatgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTCTTGAAGGTCCATGGTCCCAGAACAATCTTGATAATGGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- gcatttc
- - - - - - tatgcaa
- - - - - - - - - - - - -ttgttgg
- - - - - - - - - - - - - - - - - -aatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatttg