Sequence
atgc intronic sequence ATGC exonic sequence...ccatcacaaatagaaatggaaaacacaatgtggcttttgttttctggtctaagttgtacttggctgattcttgatgtttctatattgtttacttgagcagGTGCAGGTGGTGGTCATGCTCCAGATATAATCAAAGTATGTGGTATGAAAAATGTCCTGCCCTCATCAACAAACCCAACGCGCCCTTTTACTGTCAATAC
Basic information
| species | Glycine max |
| transcript | GLYMA08G10850.1 |
| intron # | 14 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G10850.1 (Glycine max), 3'ss of exon 14
lower sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 15
----ccatcacaaatagaaatggaaaac-acaatgtggcttttgttttctggt-cta-agttgtacttggctgattcttgatgtttctatattgtttacttgagcagGTGCAGGTGGTGGTCATGCTCCAGATATAATCAAAGTATGTGGTATGAAAAATGTCCTGCCCTCATCAACAAACCCAACGCGCCCTTTTACTGTCAATAC
| | | | | | | | | ||||| | || ||| || | || | || || || | | | || || || |||| || | | ||| ||||||||||||||||||||||| || |||||||||||||| |||||||||| | ||||| |||||||| ||||| || || |||||| |
ttttgtgttatacagacccttctattgttatattgtggatattcgtttatgatactgtaaatgggactgactaagttataat-ttactgccttgtaaaca-gTGAAGGAGCAGGTGGTGGTCATGCTCCAGACATTATCAAAGTATGTGGAGTGAAAAATGTGTTACCCTCTTCAACAAATCCAACTCGGCCATTTACTTTG-----
upper sequence: GLYMA08G10850.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 12
ccatcacaaatagaaatggaaaacacaatgtggcttttgttttctggtc-taagttgtacttggctgattcttgat-gtttctatattgtttacttga----gcagGTGCAGGTGGTGGTCATGCTCCAGATATAATCAAAGTATGTGGTATGAAAAATGTCCTGCCCTCATCAACAAACCCAACGCGCCCTTTTACTGTCAATAC
|| || | | | | || | | || | | |||||| || | || | || | | || ||| | | || | |||||| ||||| |||||||||||||| || |||||||| ||||| | |||||||| ||||||| |||||||| || || || || |||||| ||
-tattgttgtctactttgtagtgtcaatatttatctgtgatatgtgttaatggattgtacctgtcaattttctcatcatgttcttactgtcttgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACT-TCG----
upper sequence: GLYMA08G10850.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 12
---ccatcacaaatagaaatggaaaacacaatgtggc-ttttgttttctggtctaagttg--tacttggctgattcttgatgtttctatattgtttacttgagcagGTGCAGGTGGTGGTCATGCTCCAGATATAATCAAAGTATGTGGTATGAAAAATGTCCTGCCCTCATCAACAAACCCAACGCGCCCTTTTACTGTCAATAC
| | |||| | | | | | || |||| || |||| | || || |||| | | |||| ||| || || | | |||||| ||||||||||||||||||||||| ||||||||||||||| |||||||||| || |||||||| ||||||||||| || ||||| ||| |
ttttctaattttctgaaaataagatagattctatagccttttacattttggtttctttttgtcacacttttgatgcat-atgtcggtatctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCC----- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtctaagttgtacttggctgattcttgatgtttctatattgtttacttgagcagGTGCAGGTGGTGGTCATGCTCCAGATATAATCAAAGTATGTGGTATGAAAAATGTCCTGCCCTCATCAACAAACCCAACGCGCCCTTTTACTGTCAATAC
tcttgat putative branch site (score: 4)
tttactt putative PPT
tttctatattgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccatcacaaatagaaatggaaaacacaatgtggcttttgttttctggtctaagttgtacttggctgattcttgatgtttctatattgtttacttgagcagGTGCAGGTGGTGGTCATGCTCCAGATATAATCAAAGTATGTGGTATGAAAAATGTCCTGCCCTCATCAACAAACCCAACGCGCCCTTTTACTGTCAATAC
ccatcac
- - - - aatagaaa
- - - - - - - - - - aaacaca
- - - - - - - - - - - - - - -gtggctt
- - - - - - - - - - - - - - - - - - - - tttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctga
