Sequence
atgc intronic sequence ATGC exonic sequencegtagcgatgttgctgtagcttttttttaatgcatttttgttattgtcagcaatataacctgcctccgttgttgcagACTATATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAATTGGGCCACACAAAACTCAGTTTAGAAGGGATGAAAACTACG
Basic information
species | Glycine max |
transcript | GLYMA12G29450.3 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G29450.3 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G179732_T03 (Zea mays), 3'ss of exon 3
------gtagcgatgttgctgtagcttttttttaatgcatttttgttattgtcagcaatataacctgcctccgttgttgcagACTATATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAATTGGGCCACACAAAACTCAGTTTAGAAGGGATGAAAACTACG
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gtatgaatattgacgctactacacattcacttttaca-atagtgattcttctttgtatgacaacct-----catatgtgcagATTGTACAAAGCTTACCAAAAATTGTATGCATCCATGCATGATAAAGCAACTGGTCCACACAAAACTCAATTCAGAAGAGATGAGGATTATG
upper sequence: GLYMA12G29450.3 (Glycine max), 3'ss of exon 11
lower sequence: AT2G28390.1 (Arabidopsis thaliana), 3'ss of exon 11
gtagcgatgttgctgtagcttttttttaatgcattt--ttgttattgtcagcaatataac-ctgcctccgt-----tgttgcagACTATATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAATTGGGCCACACAAAACTCAGTTTAGAAGGGATGAAAACTACG
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---gtaaaattcatgaaactccatgggaaaccaagtgattagtatttggaatggaaaagtactgatgtagtagttgtgttgcagTCTATATCGAGCATACCAGAAACTTTATGCTTCAATGCATGTAAAAGGATTGGGACCCCACAAGACTCAATATAGAAGAGATGAAAACTACA
upper sequence: GLYMA12G29450.3 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------------------gtagcgatgttgctgtagcttttttttaatgcatttttgttattgtcagcaatataacctgcctccgttgttgcagACTATATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAATTGGGCCAC---ACAAAACTCAGTTTAGAAGGGATGAAAACTACG
| | || |||| | | | | | | | |||||| |||||| || ||||| | ||| | ||||||| ||||||||||||||||||| |||| ||| ||||||||||||| |||| | || || | | ||||| ||||||||||||||||||||||| |
gtaaaagtgttaaatctttgtgtcaacttcactggacatgagttctgggttcttttctgttgtctatgtctt-ttctgctttgttgctgtcaggaaaataacaagt-tcctcttttgcagATTATATAGAGCTTACCAGAAGCTTTATGCTTCCATGCATGATAGAGGAGTGGGCCCCCCCCATAAAACACAGTTTAGAAGGGATGAAAACTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttaatgcatttttgttattgtcagcaatataacctgcctccgttgttgcagACTATATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAATTGGGCCACACAAAACTCAGTTTAGAAGGGATGAAAACTACG
atataac putative branch site (score: 3)
cctccgtt putative PPT
atttttgttattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcgatgttgctgtagcttttttttaatgcatttttgttattgtcagcaatataacctgcctccgttgttgcagACTATATAGAGCTTACCAGAAACTTTTTGCATCCATGCATGATAAAGGAATTGGGCCACACAAAACTCAGTTTAGAAGGGATGAAAACTACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA