Sequence
atgc intronic sequence ATGC exonic sequencegtgtgggatttatcattgcttctaaacataacaattccttgtagtttagtggccaaaatgttattgtggcacctgttgacattcaatgatattttttcagATATTTACAAACTTCCTTTCAAGTGTGATGATTCATGCAACCCGACCTTTTGTGGTTAATGAATGGATTCAAACAAAGATTGAAGGATATGAGGTTTCTG
Basic information
species | Glycine max |
transcript | GLYMA01G02840.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G028914_T02 (Zea mays), 3'ss of exon 9
gtgtgggatttatcattgcttctaaacataacaattccttgtagtttagtggccaaaatgttattgtggcacctgttgacattcaatgatattt-tttcagATATTTACAAACTTCCTTTCAAGTGTGATGATTCATGCAACCCGACCTTTTGTGGTTAATGAATGGATTCAAACAAAGATTGAAGGATATGAGGTTTCTG
| |||| | | | | || | ||| ||||| || | | || | |||| || ||||| ||||| |||||||| |||||||| ||||| ||||||| || || ||||| || ||||||||||| | ||||||| || || ||| || ||||
-------------------------gtactacaaagcatgttgctgatatgattcatttgt-gctgtgg----tgctaatatctatcataatttgttgcagATTTTTACTAACTTCCTCTCAAGTGTCATGATCAATGCAACACGCCCATTTGTAGTCAATGAATGGATCGATGCAAAGATAGATGGTGTTGATGTCTCTG
upper sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------------------------------gtgtgggatttatcattgcttctaaacataacaattccttgtagtttagtggccaaaatgttattgtggcacctgttgacattcaatgatattttttcagATATTTACAAACTTCCTTTCAAGTGTGATGATTCATGCAACCCGACCTTTTGTGGTTAATGAATGGATTCAAACAAAGATTGAAGGATATGAGGTTTCTG
| || | || | || || | | ||||| |||| || || || || || | || | | | || ||||| || |||||||| ||||||||||| ||||||||||||||||| || ||||| | ||||| ||||||||||||||||| ||||| ||||| || ||||
gtgaaacctaattctcattttaattactggtttcttcggaatatccactgttagctttagacgttccttttcct----gttttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
upper sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0313g00020.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------------gtgtgggatttatcattgcttctaaacataacaattccttgtagtttag---tggccaaaatgttattgtggcacctgttgacattcaa---tgatattttt-----------tcagATATTTACAAACTTCCTTTCAAGTGTGATGATTCATGCAACCCGACCTTTTGTGGTTAATGAATGGATTCAAACAAAGATTGAAGGATATGAGGTTTCTG
|| | || | | || ||| | | | | | ||| | || | | | ||| | | | | | || |||| ||||| |||||||| ||||| ||||| ||||||| ||||| |||||||| || |||||||| || ||||||||||||||||| | |||||||| ||||| |||||||
gtgcaaatttgtccatttaacacactgctatttatgaaacacacattttggttttcctgcatgcccaattatgtttcttttgccttgttccctcttcagatatggatcttacttatttcaaagcctgatttttttgcttatcatatccagATATTCACAAATTTCCTCTCAAGTGCAATGATCCATGCAACTCGGCCTTTTGTTGTGAATGAATGGATTCAAACCAGAATTGAAGGCTATGAAGTTTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagtggccaaaatgttattgtggcacctgttgacattcaatgatattttttcagATATTTACAAACTTCCTTTCAAGTGTGATGATTCATGCAACCCGACCTTTTGTGGTTAATGAATGGATTCAAACAAAGATTGAAGGATATGAGGTTTCTG
tgttgac putative branch site (score: 3)
tattttttc putative PPT
attcaatgatattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgggatttatcattgcttctaaacataacaattccttgtagtttagtggccaaaatgttattgtggcacctgttgacattcaatgatattttttcagATATTTACAAACTTCCTTTCAAGTGTGATGATTCATGCAACCCGACCTTTTGTGGTTAATGAATGGATTCAAACAAAGATTGAAGGATATGAGGTTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG