Sequence
atgc intronic sequence ATGC exonic sequence...taggcatgaaacctaaattaaaacaactaccaattacctttcaagcatcttattatacatcttcctaaccatttcccctttgtgactttttgttgcacagATTTCTTCCCTTGCCAGAAGGTGCTCTTTGTTTGCTTGCTGCCTCAGCATTCACTGCAGAGTACCTTCTTTTCTACTTCCATTCAACAACACACAAGGGC
Basic information
species | Glycine max |
transcript | GLYMA09G34530.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G34530.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0033g00010.t01 (Vitis vinifera), 3'ss of exon 1
--taggcatgaaacctaaattaaaacaactaccaattacctttcaagcatcttattatacatcttcctaaccatttccc-ctttgtgactttttgttgcacagATTTCTTCCCTTGCCAGAAGGTGCTCTTTGTTTGCTTGCTGCCTCAGCATTCACTGCAGAGTACCTTCTTTTCTACTTCCATTCAACAACAC-ACAAGGGC
|| | | || ||||||| || | | ||| || ||| | |||| |||| || | | | | || || ||| || |||||||||||||||| ||||| || ||| |||||||| |||| ||| |||||||||| | || ||||| |||||||||||||||| | || ||
tgattgctcttgatcggcctttttacaactagaaacagcaatgcaataatgagatttt-catcag--taactatggctgaccatattttttcccttttttcagCTTAGTTCCCTTGCCAGAAGGAGCTCTCTGCTTGATTGCTGCCACAGCGTTCTCTGCAGAGTATTTCCTATTCTATTTCCATTCAACAACACCATAAAGG- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcttattatacatcttcctaaccatttcccctttgtgactttttgttgcacagATTTCTTCCCTTGCCAGAAGGTGCTCTTTGTTTGCTTGCTGCCTCAGCATTCACTGCAGAGTACCTTCTTTTCTACTTCCATTCAACAACACACAAGGGC
tcctaac putative branch site (score: 1)
ctttttgtt putative PPT
tattatacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taggcatgaaacctaaattaaaacaactaccaattacctttcaagcatcttattatacatcttcctaaccatttcccctttgtgactttttgttgcacagATTTCTTCCCTTGCCAGAAGGTGCTCTTTGTTTGCTTGCTGCCTCAGCATTCACTGCAGAGTACCTTCTTTTCTACTTCCATTCAACAACACACAAGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- -gcatgaa
- - - - - - - - - -aaaacaa
- - - - - - - - - - - - - ctaccaa
- - - - - - - - - - - - - - - - - - - -ttcaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgactt