Sequence
atgc intronic sequence ATGC exonic sequencegttttgaagctttctttgtttgtgtaccttttactctaatttccaatctgataataaattcttgttaattgaattctggtgattgttttcttttcctttagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAGACTAGGAAAGGAAGACAAG
Basic information
species | Glycine max |
transcript | GLYMA06G05170.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G146688_T01 (Zea mays), 3'ss of exon 2
------gttttgaagctttctttgtttgtgtaccttttactctaatttccaatctgataataaattcttg--ttaattgaattctggtgattgttttc----ttttcctttagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAGACTAGGAAAGGAAGACAAG
| | || | | | | || || || | || | | || | | || | | | | |||||||| ||||| || |||||||| ||||| ||||||| || || |||||||||||||| |||| ||||| || | ||||
gtacgtacgtacacgccgccgtgtcgagctagttgactggtccgtccgcccgtccgtccatggagctgaagctgaagttgaaactaaaactaaaactgaaagtaattaagcagGCATAGGTGGACGGGGAGGTATGAGGCGCACCTGTGGGACAACAGCTGCAAGAAGGAAGGCCAGAGCAGGAAGGGCCGGCAAG
upper sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G028151_T01 (Zea mays), 3'ss of exon 2
---------------------gttttgaagctttctttgtt-tgtgtaccttttactc-taatttccaat-ctgataataaattcttgttaattgaattctggtgattgttttcttttcctt--tagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAGACTAGGAAAGGAAGACAAG
|| | || || ||| | | || | | ||| | | | | | | | || | ||| || | | | |||||||| ||||| || |||||||| ||||| | ||||| || || |||| ||||||||||||||| ||||||| | ||||
gtatcctcccaactcccgaccgtccgtacgccgtcgctgtcgcaggcgcgcgcgacccgcagcatccggcgcccgtgcgatcgagtcgctcactggccgc--gtggtttcccaccgtgcaaaagcagGCATAGGTGGACGGGGAGGTATGAGGCGCACCTCTGGGACAACAGCTGCAGGAAGGAAGGGCAGACCCGGAAAGGCCGGCAAG
upper sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
gttttgaagctttctttgtttgtgtaccttttactctaatttccaatctgataataaattcttgttaattgaattctggtgattgttttcttttcctttagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAGACTAGGAAAGGAAGACAAG
||| ||| ||| | || || | | ||| | | || ||| ||||| | | | | | | || | | || ||||||||||||||||| |||||||| ||| | ||||| ||||||| |||||||||||| || | ||| |||||||||||||
------gttgtttttttattt-tataatattaaactttgtttgactttcgttagtaa-----tgttacatatacttacttaaaaggtta--tgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
upper sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------------------------------------------------gttttgaagctttctttgtttgtgtaccttttactctaatttccaatctgataata----aattcttgttaattgaattctggtgattgttttcttttcctttagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAGACTAGGAAAGGAAGACAAG
|| ||| | | | ||| | || || | ||| ||| | ||| |||| | | | ||| | | | | ||| ||| || |||||||||||||||||||| |||||||| ||| | ||||||||||||||||||||||| |||||||||||||||||||||||||
gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctg-ctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttcccc--agGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgataataaattcttgttaattgaattctggtgattgttttcttttcctttagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAGACTAGGAAAGGAAGACAAG
tgttaat putative branch site (score: 3)
ttgttttcttttcctt putative PPT
taataaattcttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttgaagctttctttgtttgtgtaccttttactctaatttccaatctgataataaattcttgttaattgaattctggtgattgttttcttttcctttagGCATAGATGGACTGGTAGGTATGAAGCGCATTTGTGGGATAATAGTTGCAAGAAGGAAGGGCAGACTAGGAAAGGAAGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA