Sequence
atgc intronic sequence ATGC exonic sequence...tttgcctcaaaggcaaagcttcattaatttcttactcattgtcggttcagtattgtgcttgccttttatattctaatgtacttttcctttttcactacagATGAATTGTGCTCACCTGGAAAATTGTTTGCATGAGGCAAGAGAGGAAGCTCAGACACAAAAAAGTTCTGCTGACAGGAGGGCCTCTGAGTATAGTTTAC
Basic information
species | Glycine max |
transcript | GLYMA02G36800.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G36800.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G143445_T01 (Zea mays), 3'ss of exon 2
-tttgcctcaaaggcaaagcttcattaatttc-ttactcattgtcggtt-cagtattgtgcttgccttttatattc--taatgtacttttcctttttcac-------tacagATGAATTGTGCTCACCTGGAAAATTGTTTGCATGAGGCAAGAGAGGAAGCTCAGACACAAAAAAGTTCTGCTGACAGGAGGGCCTCTGAGTATAGTTTAC
|| | | ||| || || ||| | | | ||| || | || | | ||| | | |||| | ||||| || ||| | | || | |||||||||||||| ||||| ||||| ||||| ||||| |||||||| || || | ||| | ||| |||| |||||||| ||||| ||||||| | |
gttagtcataaa----aatctatgataactccactgctctgtgcaaatcgcaatgatcaccttccatattatttctgtgaatgtgattctccctctacatattttgatgcagATGAATTGTGCGCACCTTGAAAACTGTTTACATGAAGCAAGAGAAGAGGCCCGAACAAACAAATGTTCAGCTGACAGAAGGGCTGTTGAGTATGATGCTC
upper sequence: GLYMA02G36800.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0037g00730.t01 (Vitis vinifera), 3'ss of exon 3
tttgcctcaaaggcaaagcttcattaatttcttactcattgtcggttcagtattgtgcttgccttttatattctaatgtacttttc--ctttttcactacagATGAATTGTGCTCACCTGGAAAATTGTTTGCATGAGGCAAGAGAGGAAGCTCAGACACAAAAAAGTTCTGCTGACAGGAGGGCCTCTGAGTATAGTTTAC
||| || |||| | || |||| | ||| | | | | ||| || | || | |||| | | | | | | | ||||||||||||||||||| |||| |||||| | ||||| |||||||||||||||||||| || || |||||||| |||||||||| ||||||||| |
cttgtcttt--ggcagcattagtttgattttatcatcacagacatgtttgaattctgacttttttccactttctcttctctctgtggacactctgttaacagATGAATTGTGCTCACTTGGAGAATTGTCTACATGAAGCAAGAGAGGAAGCTCAGACTCACCTCTGTGCTGCTGACCGGAGGGCCTCGGAGTATAGTGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcagtattgtgcttgccttttatattctaatgtacttttcctttttcactacagATGAATTGTGCTCACCTGGAAAATTGTTTGCATGAGGCAAGAGAGGAAGCTCAGACACAAAAAAGTTCTGCTGACAGGAGGGCCTCTGAGTATAGTTTAC
ttctaat putative branch site (score: 2)
tacttttcctttttca CT-rich tract
ttttatattctaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgcctcaaaggcaaagcttcattaatttcttactcattgtcggttcagtattgtgcttgccttttatattctaatgtacttttcctttttcactacagATGAATTGTGCTCACCTGGAAAATTGTTTGCATGAGGCAAGAGAGGAAGCTCAGACACAAAAAAGTTCTGCTGACAGGAGGGCCTCTGAGTATAGTTTAC
- - cctcaaa
- - - - - - - - agcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgcc