Sequence
atgc intronic sequence ATGC exonic sequencegtatacatttatgtcttcatcatatggcattggaatttctattcaatttattgattaatttgaattttgtaaatgaaactatacagTCAGTTGCCAGACTTTCTGGGTGGTTCTTGTACATGTGCTGCAGAAGGTGGATGTCTTCGGTCTAACAAGGGTCCATGGAATGATCCTGACATCATGAAG
Basic information
species | Glycine max |
transcript | GLYMA06G48060.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G48060.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G010834_T01 (Zea mays), 3'ss of exon 6
gtatacatttatgtcttcatcatatggcattggaatttctattca-atttattg------attaatttgaattttgtaaa-------tgaaactatacagTCAGTTGCCAGACTTTCTGGGTGGTTCTTGTACATGTGCTGCAGAAGGTGGATGTCTTCGGTCTAACAAGGGTCCATGGAATGATCCTGACATCATGAAG
|||| ||| | | | ||||| | || ||| | | ||| |||| || ||| ||| | | | ||||| | || || ||| |||| || | || || |||||||| | || |||||| | |||||||||| ||||||||||||||||| || || ||||||
gtattt-tttctattacaaccatattaagcataatttctcgatcataatgattatgtcccattagcttagattgtgtgtgttttcttttgatgttggtagTCAACTTCCTGAATTTTTGGGGGGGACATGCACTTGTGCTGCTGTGGGAGGATGTATGAGGTCTAACAAAGGTCCATGGAATGATCCAGATATTATGAAG
upper sequence: GLYMA06G48060.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 8
-----------gtatacatttatgtcttcatcatatggcattggaatttcta-ttcaatttattgattaatttgaattttgtaaatgaaact----atacagTCAGTTGCCAGACTTTCTGGGTGGTTCTTGTACATGTGCTGCAGAAGGTGGATGTCTTCGGTCTAACAAGGGTCCATGGAATGATCCTGACATCATGAAG
|||| ||| || | ||| |||| ||||||| ||| |||| || || || || | | || | |||||| |||| ||||| ||||||| ||||| ||||||||| | || ||||| || || ||||||| || |||||||||||||||||||| || ||||||
gtttgtgtttcacgctcattc-tgttttgttaatactccattttgatttctaattctatttgttccttgcatttttcttcattttttccccttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaatttctattcaatttattgattaatttgaattttgtaaatgaaactatacagTCAGTTGCCAGACTTTCTGGGTGGTTCTTGTACATGTGCTGCAGAAGGTGGATGTCTTCGGTCTAACAAGGGTCCATGGAATGATCCTGACATCATGAAG
gattaat putative branch site (score: 3)
tattcaatttattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatacatttatgtcttcatcatatggcattggaatttctattcaatttattgattaatttgaattttgtaaatgaaactatacagTCAGTTGCCAGACTTTCTGGGTGGTTCTTGTACATGTGCTGCAGAAGGTGGATGTCTTCGGTCTAACAAGGGTCCATGGAATGATCCTGACATCATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA