Sequence
atgc intronic sequence ATGC exonic sequence...agattcaagacacttgaattgtttcactttcattcatttatttatttattttcattaaatgacttaccgtttaaggagtgtggttatctttcctttgtagGTGGAAATCAAGAAGGCAGAACCAAAGAAGCCAAATCCACCAGCTCCATCATCCAAGCGCTATAATGACTCCCGGTCTTCATATGGTGGCGGATATGGAG
Basic information
species | Glycine max |
transcript | GLYMA19G10300.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G10300.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g38410.3 (Oryza sativa), 3'ss of exon 5
---agattcaagacacttgaattgtttcactttcattcatttatttatttattttcattaaatgacttaccgtttaaggagtgtggttatctttcctttgtagGTGGAAATCAAGAAGGCAGAACCAAAGAAGC---CAAATCCACCAGCTCCATCATCCAAGCGCTATAATGACTCCCGGTCTTCATATGGTGGCGGATATGGAG---
|| | ||| | | | | ||| | || || | | | | ||| | || | | ||| || || ||||||||||||| |||||||| |||||||||||||| ||||||||||| |||||||| | || || ||| | || |||||||| | | | | | |
gacagctgtgctgttgttgtagaatgtgatgctcaa-cgggtaattggtagcaaggacgtataggtttatattgatagaacttcggtcat--ttgctttgtagGTGGAGATCAAGAAAGCAGAACCAAAGAAATCCTCAAATCCACCA---CCATCATC---ACATGGTAGTGCCTCTAGATCAGCATATGGTAGGGATTCTAGGGGTC
upper sequence: GLYMA19G10300.1 (Glycine max), 3'ss of exon 5
lower sequence: AC233867.1_FGT004 (Zea mays), 3'ss of exon 3
agattcaagacacttgaattgtttcactttcattcatttatttatttattttcattaaatgactta--ccgtttaa--ggagtgtggttatct--ttcctttgtagGTGGAAATCAAGAAGGCAGAACCAAAGAAGC---CAAATCCACCAGCTCCATCATCCAAGCGCTATAATGACTCCCGGTCTTCATATGGTGGCGGATATGGAG
||| || | |||| | | | | | || ||| | || | | || ||| | | ||| || | || |||||||||||| |||||||| |||||||||||||| | ||| ||||| | ||| || | || | | ||| |||||| | | || | |
----ctaagtcatc--agttgtgctattccatggaaaatcatgcttaattgatagaaagggccataggttatttgaccaagcttaggtcatttgctttgtttgtagGTGGAGATCAAGAAAGCAGAACCAAAGAAATCCTCCAATGCACCACCACCACCACCATTATATGGTAGAAATGCTAGGTTAGCATATGATAGTGGCTCTA---
upper sequence: GLYMA19G10300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G050218_T01 (Zea mays), 3'ss of exon 5
agattcaagacacttgaattgtttcactttcattcatttatttatttattttcattaaatgacttaccgttta------aggagtgtggttatctttcct-----ttgtagGTGGAAATCAAGAAGGCAGAACCAAAGAAGCCAAATCCACCAGCTCCATCATCCAAGCGCTATAATGACTCCCGGTCTTCATATGGTGGCGGATATGGAG
|| || |||| | |||||| | | ||| || || | | | | ||| ||| | ||| || | | ||||||||||| |||||||| |||||||||||||| | || | ||| || | || || | | |||| |||||| | |||| | | |||
---------tcatctg--ttgtgctaatttcatggagcatcatgcttaattaataggaaggccccataggttatttgacagggcttaggtcatttgctttgtttgttgtagGTGGAGATCAAGAAAGCAGAACCAAAGAAATCCTCCAATGCACCGCCACCACCAGTGCATGTTAGAAATGCTAGGTCAGCATATGATAGCGGCTCTAGAG
upper sequence: GLYMA19G10300.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0066g00480.t01 (Vitis vinifera), 3'ss of exon 5
agattcaagacacttgaattgtttcactttcattcatttattta---tttattttcattaaatgacttaccgtttaaggagtgtggttatct-ttcctttgtagGTGGAAATCAAGAAGGCAGAACCAAAGAAGCCAAATCCACCAGCTCCATCATCCAAGCGCTATAATGACTCCCGGTCTTCATATGGTGGCGGATATGGAG
| || || ||| | | | | | ||| | | | | | | ||| | |||| || | ||| | | | | ||| ||||||||||| |||||||| |||||||||||||||||||| ||||||| || |||||| ||| ||| || || | || | |||||| || | |||||
---tgcatgatgtatga-taatctggatctgatttctgtttacaagatgcagtttgtgtgtatgaagtatgataatcttagtccgaatttttgttcacttgtagGTGGAGATCAAGAAAGCAGAACCAAAGAAGCCAAACCCACCAGTGCCCCCATCCAGGCGATATTCGGATTCTAGACCTGGCTTTGGTGGGGGCTTTGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattttcattaaatgacttaccgtttaaggagtgtggttatctttcctttgtagGTGGAAATCAAGAAGGCAGAACCAAAGAAGCCAAATCCACCAGCTCCATCATCCAAGCGCTATAATGACTCCCGGTCTTCATATGGTGGCGGATATGGAG
gacttac putative branch site (score: 2)
ttatctttcctttgt putative PPT
ttcattaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agattcaagacacttgaattgtttcactttcattcatttatttatttattttcattaaatgacttaccgtttaaggagtgtggttatctttcctttgtagGTGGAAATCAAGAAGGCAGAACCAAAGAAGCCAAATCCACCAGCTCCATCATCCAAGCGCTATAATGACTCCCGGTCTTCATATGGTGGCGGATATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - cacttga
- - - - - - - - - - - - - - - cattcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagtgtg