Sequence
atgc intronic sequence ATGC exonic sequence...aaacacacacacatgcaagtctaacatgtttacttggtttgtgtttggaaacttgttatcatattcatatatctttatcattgtgttttttgctttacagAATGCTGTCTCTCAGAAGGGAAATGAAGTGAATTTGACCCTTGGTGGCATTGACCTCAACAATTCAGGCAG
Basic information
species | Glycine max |
transcript | GLYMA04G09780.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09780.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G019153_T01 (Zea mays), 3'ss of exon 5
aaacacacacacatgcaagtctaacatgtttacttggtttgtgtttggaaact-tgt-tatcatattcatatatctttatcattgtgttttttgctttacagAATGCTGTCTCTCAGAAGGGAAATGAAGTGAATTTGACCCTTGGTGGCATTGACCTCAACAATTCAGGCAG
|||| | |||||| || | | | || | | | || | | | | ||| | || | || ||| | | |||| ||| |||||||| || ||||||||||| ||||||||||| || || ||||| || ||||| |||||||||||||||||
--ccacattcccatgcactactcaatttctctctctctctcttgctgcattttgtatgtataaggttttagaagattaatctacttttgttttacttctcagAATGCCGTTTCTCAGAAGGGGAATGAAGTGAACTTAACTCTTGGCGGTATTGATCTCAACAATTCAGGCAG
upper sequence: GLYMA04G09780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G24580.1 (Arabidopsis thaliana), 3'ss of exon 4
aaacacacacacatgcaagtctaacatgtttacttggtttgtgtttgg---aaacttgttatcata---ttcatatatctttatcattgtgttttttgctttacagAATGCTGTCTCTCAGAAGGGAAATGAAGTGAATTTGACCCTTGGTGGCATTGACCTCAACAATTCAGGCAG
| | | || || || | || | | ||| | | || ||| |||||| | | | ||||| | || | | || | | | |||| ||| ||| |||||||| | ||| || ||| |||||||||| || ||||| |||||||||||||||||
----agagattggtgaaaatcctatat-cagaaatattttttataaggcatgaacctgttattacagagtatgagtatctcaaatttt-tctgttctattcttcagAGTGCAGTCCAACAGAAGGGCAGTGAGGTCAATCTGACCCTTGGGGGAATTGATCTCAACAATTCAGGCAG
upper sequence: GLYMA04G09780.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g07310.t01 (Vitis vinifera), 3'ss of exon 3
--------aaacacacacacatgcaagtctaacatgtttacttggtt--tgtgtttggaaacttgttatcatattcatatatctttatcattgtgttttttgctttacagAATGCTGTCTCTCAGAAGGGAAATGAAGTGAATTTGACCCTTGGTGGCATTGACCTCAACAATTCAGGCAG
| | || | | |||| | | ||| | || || || ||| || || | | ||||| ||| || |||| |||| |||| | |||| ||||| | ||| |||||||||||||||||||| |||||||||||||||||||||||
ttttatttgatgatactctttttcaagctctatctttttccatgcttgttgcatttttaaggttttagaaggttacatatgctactat----------ttctctttccagAGTGCTATTCCTCAAAAGGGTAGTGAGGTGAATTTGACCCTTGGTGGTATTGACCTCAACAATTCAGGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaaacttgttatcatattcatatatctttatcattgtgttttttgctttacagAATGCTGTCTCTCAGAAGGGAAATGAAGTGAATTTGACCCTTGGTGGCATTGACCTCAACAATTCAGGCAG
ttttttgcttt CT-rich tract
ttatcatattcatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaacacacacacatgcaagtctaacatgtttacttggtttgtgtttggaaacttgttatcatattcatatatctttatcattgtgttttttgctttacagAATGCTGTCTCTCAGAAGGGAAATGAAGTGAATTTGACCCTTGGTGGCATTGACCTCAACAATTCAGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- acacaca
- - - - - - -tgcaagt
- - - - - - - - - - - - catgttt
- - - - - - - - - - - - - - - - - - gtttgtg