Sequence
atgc intronic sequence ATGC exonic sequence...agtctgttttcattgtcgtatttttaaaaaaaatatttattgcatttttaaaaaaaattgtgaaatgatgatgaaattaggggttttgacttaattgaagGCATAGGTGGACGGGGAGGTATGAGGCTCACCTGTGGGATAATAGTTGTAGAAGAGAGGGACAAACTCGCAAAGGAAGGCAAG
Basic information
species | Glycine max |
transcript | GLYMA18G47980.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47980.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g40070.1 (Oryza sativa), 3'ss of exon 2
-agtctgttttcattgtcgtatttttaaaaaaaatatttattgcatttttaaaaaaaattgtgaaatgatgatgaaattaggggttttgac----ttaattgaagGCATAGGTGGACGGGGAGGTATGAGGCTCACCTGTGGGATAATAGTTGTAGAAGAGAGGGACAAACTCGCAAAGGAAGGCAAG
| | | || || | | |||| | | || || | || || | | | | | | || | | | |||| || || |||||||| ||||| ||| | ||||||||||| || ||||||||||| ||||||||||| || || | |||||| || |||||||
caaccaatgtttat-atttttttttcagacgtgattttga----atcttaatagcatgcatatgagctttagtaaattacctgctcttgaaattgttggtttcagGCATAGATGGACAGGGCGATATGAGGCTCATCTCTGGGATAATAGCTGTAGAAGAGAAGGGCAGAGTCGCAAGGGTAGGCAAG
upper sequence: GLYMA18G47980.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g42570.1 (Oryza sativa), 3'ss of exon 2
agtctgttttcattgtcgtatttttaaaaaaaatatttat-tgcatttttaaaaaaaattgtgaaatgatgatg----aaattaggggttttgacttaattgaagGCATAGGTGGACGGGGAGGTATGAGGCTCACCTGTGGGATAATAGTTGTAGAAGAGAGGGACAAACTCGCAAAGGAAGGCAAG
| ||||| || | || | ||||| ||||| ||| ||| || ||||| || | | | | || ||| | | || || || |||||||| ||||| || || ||||| ||||| |||||||||||||| ||||| ||||| || |||| |||||| || || || |
---caattttc-ttctagt-cgataaaaaataatatatatgcatgtttatataaaaatttttaagttcttcatacgtataatcacgttgttaatctgtctttcagGCATAGATGGACAGGAAGATATGAAGCTCATCTGTGGGATAATAGCTGTAGGAGAGAAGGCCAAAGTCGCAAGGGGAGACAGG
upper sequence: GLYMA18G47980.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G366434_T01 (Zea mays), 3'ss of exon 2
agtctgttttcattgtcgtatttttaaaaaaaatatttattgc--atttttaaaaaaaattgtgaaatgatgatgaaattaggggttttgacttaattgaagGCATAGGTGGACGGGGAGGTATGAGGCTCACCTGTGGGATAATAGTTGTAGAAGAGAGGGACAAACTCGCAAAGGAAGGCAAG
| | | | || ||| | | | | || | || ||| |||| | || |||| | || || ||| || |||||||| ||||| ||| ||||||||||||| || |||||||||||||||||||| || || || | |||||| || |||||||
tatatatatatatatatatatacgtgttgaggttggtaataacaaatgtttttgaaaacgcactatatatatgcataattttgagtatt--cttgtttacagGCATAGATGGACAGGGCGGTATGAGGCTCATCTATGGGATAATAGTTGTAGAAGGGAAGGGCAGAGTCGCAAGGGTAGGCAAG
upper sequence: GLYMA18G47980.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 1
agtctgttttcattgtcgtatttttaaaaaa-aatatttattgcatttttaaaaaaaattgtgaaatgatgatgaaattaggggttttg---acttaattgaagGCATAGGTGGACGGGGAGGTATGAGGCTCACCTGTGGGATAATAGTTGTAGAAGAGAGGGACAAACTCGCAAAGGAAGGCAAG
| | | ||||| | | | || | || || ||| |||| || || ||| | | ||| |||||| | ||||| || |||| |||||||| |||||||| |||| |||||||| || || |||||||||||||| | ||||
----ggcgcagagagctaaattttagcctggcgaaggtcgaagttgttgagggtcatatcctggtctgaggatgttggggggtgtattgtgtgttgatttgtagGCATCGTTGGACTGGACGGTACGAGGCTCATCTGTGGGACAATACTTGTAGAAAGGAAGGTCAAACTCGCAAAGGTCGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaaaaaaaattgtgaaatgatgatgaaattaggggttttgacttaattgaagGCATAGGTGGACGGGGAGGTATGAGGCTCACCTGTGGGATAATAGTTGTAGAAGAGAGGGACAAACTCGCAAAGGAAGGCAAG
aaaaaaattgtgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtctgttttcattgtcgtatttttaaaaaaaatatttattgcatttttaaaaaaaattgtgaaatgatgatgaaattaggggttttgacttaattgaagGCATAGGTGGACGGGGAGGTATGAGGCTCACCTGTGGGATAATAGTTGTAGAAGAGAGGGACAAACTCGCAAAGGAAGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
-gtctgtt
- - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggttt