Sequence
atgc intronic sequence ATGC exonic sequencegtcagctccccttcctccaccacagtgtggaacatttgctcccaagactcattcaaaaggaatggaaattggaaaaacaaatctttatatcaatggcacacaccttacaaaatattaatttttttatgcatgtatttggtctagGCATCGGTAGAACTTCAAGGTATCAAAGGAATGTGGTCACTTAGATCCTCAACAGATGATCCTTTTGATACTTTTCTGGTTGTGAGTTTTATAAGTGAAA
Basic information
species | Glycine max |
transcript | GLYMA05G30530.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 12
gtcagctccccttcctccaccacagtgtggaacatttgctcccaagactcattcaaaaggaatggaaattggaaaaacaaatctttatatcaatggcacacaccttacaaaatattaatttttttatgcatg-tatttggtctagGCATCGGTAGAACTTCAAGGTATCAAAGGAATGTGGTCACTTAGATCCTCAACAGATGATCCTTTTGATACTTTTCTGGTTGTGAGTTTTATAAGTGAAA
|| || |||| || || | | ||| || | || | | | | | || | | | | |||| || || ||||||||||| ||||||||||||||||| | | ||| |||| ||||| | |||||||| || || || || |||||||| |||||||
--------------------------------------------------gtttggtgtatattaggattgtcaatttgtctcagtgtcatgtaagcaatattctcatctgatgtaatctaataaaactctgctgtatattgcagGCGTCCGTGGAACTTCAAGGCATCAAAGGAATGTGGTCGTTGAAATCGTCAATTGATGAAGCCTTTGATACATTCCTTGTAGTTAGTTTTATCAGTGAAA
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 11
gtcagctccccttcctccaccacagtgtggaacatttgctcccaagactcattcaaaaggaatggaaattggaaaaacaaatctttatatcaatggcaca--caccttacaaaatattaatttttttatgcatgtatttggtctagGCATCGGTAGAACTTCAAGGTATCAAAGGAATGTGGTCACTTAGATCCTCAACAGATGATCCTTTTGATACTTTTCTGGTTGTGAGTTTTATAAGTGAAA
| || | | | | || || | | ||||| || | | | | || | || | | | | | |||| || || ||||||||||||||||||||||||||||| | | ||| |||| ||||| | || ||||| ||||| ||||| || ||||| |||||||
------------------------------------------------------------gtttgatttatgcgcgaaatctcattgtcttgtatgcacaattttctcatatggtttctatatcttaaaactccgctctattacagGCGTCTGTGGAACTTCAAGGTATCAAAGGAATGTGGTCGTTGAAATCTTCAATTGATGAAGCCTTCGATACATTTCTTGTTGTTAGCTTTATCAGTGAAA
upper sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 12
gtcagctccccttcctccaccacagtgtggaacatttgctcccaagactcattcaaaaggaatggaaattggaaaaacaaatct--ttatatcaatggcacacaccttacaaaatattaatttttttatgcatgtatttggtctagGCATCGGTAGAACTTCAAGGTATCAAAGGAATGTGGTCACTTAGATCCTCAACAGATGATCCTTTTGATACTTTTCTGGTTGTGAGTTTTATAAGTGAAA
| || ||| || | |||| ||| | | | || | | | | || | | ||| | | ||| | |||||||| || ||||||||||| |||||||||||||||||| | ||||| || || |||||||| ||| || || ||||||| || ||||| ||||| |
-----------------------------------------gtctggcttatttcaaccattttcttattgatctctagaatttgactttgccatttataagttcttctaaacttgcttattaatgtgcatatgccatca-catagGCATCAGTGGAACTTCAAGGCATCAAAGGAATGTGGTCATTGAGATCTTCTACTGATGATCCACATGACACCTTCTTGGTTGTAAGCTTTATCAGTGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaatggcacacaccttacaaaatattaatttttttatgcatgtatttggtctagGCATCGGTAGAACTTCAAGGTATCAAAGGAATGTGGTCACTTAGATCCTCAACAGATGATCCTTTTGATACTTTTCTGGTTGTGAGTTTTATAAGTGAAA
tattaat putative branch site (score: 2)
ttacaaaatattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagctccccttcctccaccacagtgtggaacatttgctcccaagactcattcaaaaggaatggaaattggaaaaacaaatctttatatcaatggcacacaccttacaaaatattaatttttttatgcatgtatttggtctagGCATCGGTAGAACTTCAAGGTATCAAAGGAATGTGGTCACTTAGATCCTCAACAGATGATCCTTTTGATACTTTTCTGGTTGTGAGTTTTATAAGTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG