Sequence
atgc intronic sequence ATGC exonic sequence...cttgacttttaattcttaccatgttgtattaaatttgtgtttgcctttgcattgtttacttgaatgattgtcagtaaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGATTCCGAAAAAGACATCCCTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
Basic information
species | Glycine max |
transcript | GLYMA08G06160.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 6
---------ctt----gacttttaattc--ttaccatgttgtattaaatttgtgtttgcctttgcattgtttacttgaatgattgtcagt-aaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGATTCCGAAAAAGACATCCCTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
||| | | |||| | | ||| | || | | | || | | ||| ||| || | ||| || || ||| || ||||||| ||| || | ||||||||||||||||||||||||||| || || | | ||||| |||| || ||||| || || || || ||||| | | |
gtttgtgctcttcagaggggcatcattcagtaaatccaccctataacatgagcagatattagtaaatc-tctccttatgatattagcattgaaacttgcatttcattgtgcttcagGAAAGTAACAGGCTTGAATACTTGATTCCGAAAAAGACATCCTTGCGGTACCGCTTGCCCATGGCTGATCAAGGGTTTATCGAGTTCGTTGCGTGCCTTC
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 6
--------------------cttgacttttaattcttaccatgttgtattaaatttgtgtttgcctttgcat-tgtttacttgaatgattgtcagt-aaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGATTCCGAAAAAGACATCCCTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
| | | | | ||||| | | || | | | | || | | | ||| |||| ||| || | || || || ||| || ||||||| ||| || | || |||||||||||||||||||||||| || |||| ||||||| |||| || ||||| || || || |||||||| || | |
gtttgtgcttttcggaggggcgtcattgagtaaatttaccctataacatgagtaccttatcttatttagtagatctttccttgtgatattagcattgaagcttgcatttcattgtgcttcagGAAAGTAACAGGCTTGAGTACTTGATTCCGAAAAAGACATCCTTGCGGCACCGATTGCCCATGGCTGATCAAGGGTTTATCGAGTTTGTTGCGTACCTTC
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------cttgacttttaatt----cttacca-tgttgtatta--aatttgtgtttgcctttgcattgtttacttgaatgattgtcagtaaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGATTCCGAAAAAGACATCCCTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
||| ||| | | | || || | || | ||||||| | | ||| || | | || | ||| | | ||| | |||| | | | ||||| | ||| || || ||| | || ||||||||| |||| || |||| |||| | |||||||| |||||||||||||| |||||||| || ||||||
gtgcgtattgaaaaaccaaaaagaaagaaaactttactatatagtgcggctcacagctattactcaagcaatttgtaatggttgttgaatc-tgatttcaaactaatgt-aatgggtttgt-gtttctaatacctcagGAGAGTAACAATTTGGAGTACCTAATACCGAAAAAGTCATCGCTAAGGCGTAGACTACCAATGGGTGACCAAGGCTTCATAGACTTTGTGGCATACTTGC
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 12
-cttgacttttaattcttaccatgttgtattaaatttgtgtttgcctttgcattgtttacttgaatgattgtcagtaaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGATTCCGAAAAAGACATCCCTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
| | || || | | | || || || | ||| | | ||| || | ||| | | |||| | | ||| ||||| |||||| | | |||||| | || || |||||||||||| ||||||| | ||||||||||| |||||||||||||| ||||||||| |||| |||
atctttgtgttcatattactcctatttctgcaacttcctttttatttatttattattattattaatc-ctaaagccgtgcatgttgtccaattttcttcagGACACCAACAGACTGGAATACCTCATCCCAAAAAAGACATCCTTGAGGCACCGGTTGCCAATGGGGGACCAAGGCTTCATCGACTTTGTTTCTCATATGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgcattgtttacttgaatgattgtcagtaaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGATTCCGAAAAAGACATCCCTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
tattaat putative branch site (score: 2)
attgtcagtaaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgacttttaattcttaccatgttgtattaaatttgtgtttgcctttgcattgtttacttgaatgattgtcagtaaatttattgtttattaatctacagGAAACCAACCGGTTAGAATACTTGATTCCGAAAAAGACATCCCTGAGGCATAGATTGCCAATGGGAGACCAAGGCTTCATTGACTTTGTTGCTCACTTGC
- - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - -tttgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatga