Sequence
atgc intronic sequence ATGC exonic sequence...ctggactgacaaaattcggagaagttttaattcataatgtatatttctatattcttttctcttcaaagatcatcactaatctttttctgctaaatttcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
Basic information
species | Glycine max |
transcript | GLYMA14G03780.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os07g46590.1 (Oryza sativa), 3'ss of exon 6
ctggactgacaaaattcggagaagttttaattcataatgtatatttctatat-tcttttctcttcaaagatcatcactaatctttttctgctaaatttcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
| | | ||| | || | | | | || || ||| | || || || | |||| | || | | || ||||| || ||||||||||| || || || || || |||||||||||||| || || || |||||||||||||| ||||| |||||||| || ||
caaagaaaatagcattaacaaaacacagattcttctgcaggcacatttaaatgtctggttatttaaattattctagctaacttgattattgcatatg-cagGTCTCGCTTTTAAATATCGTTGTTGAGTTGAAAAAGTGCTGCAACCACCCATTTTTATTTGAAAGTGCTGATCATGGTTATGGTGGAGATAGCATTGGTG
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 19
-------------------------------------------------------ctggactgacaaaattcggagaagt--tttaattcataatgtatatttcta-----tattc---ttttctcttcaaaga---------tcatcactaatctttttctgctaaattt------------cagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
|| || |||||| | || | | | || ||| | || || || | | | | || |||| | | | ||| | || | || ||||| || ||| | || ||||| || ||||| ||||| |||||||||||||| ||||||||||||||||| || ||||| |||||||| || ||
gtgagccaaatctgctctcccatgtgggcaaggattgattgtttataacttcatgtctgatctactaaattcaaataattagtgtgcttggtaacaattgttcttaaggcacatccaaatctgccctccaaaaaattagtgtcctgctatcatgttttatgtgactgacttgttaatgacatgcagGTATCACTTCTTAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTCTTGTTTGAAAGTGCCGATCATGGTTATGGTGGAGATAGCATCGGTG
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 16
ctggactgacaaaattcggagaagttttaattcataatgtatatttctatattcttttctcttcaaagatcatc--actaatctttttctgctaaatttcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
|| || | | | | | | || | | || | | | ||| | | | || | || ||||| || ||||| || ||||| || ||||| ||||| |||||||||||||| || |||||||||||||| || || || |||||||| || |
-gttcctcacctcactgtgcattacctagcaaactggagcatgggcacaaggcaacacttggccattggctaccaaactgacttgatcatggcatatg-cagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 17
lower sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 18
------------------------------------------------------------------ctggactgacaaaattcggagaagttttaattcataatgtatatttctatattcttttctcttcaaagatcatcactaatctttttctgctaaatttcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
||| |||| || || || | | ||| || |||| | || | | | | || | | | ||||| | | || |||||||| |||||||| || |||||||| || ||||| |||||||| ||||| ||||| ||||||||||| |||||||| ||||| || ||| | ||
gtgagtgactttatgatgcacccaggttctcatatttattgttatgaataattattttctttgtccctgcactgt--aagttaggtgga---ttattt--taatatgcatccgacttcttaagtttgttgatattaagctaacaatctctgagttacaatcaacagGTTTCACTTTTAAACATCGTGGTGGAGTTGAAGAAATGCTGCAATCATCCTTTCTTATTTGAAAGTGCAGACCATGGATATGGGGGTGACATAAACGATA
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S93_123V6.1 (Physcomitrella patens), 3'ss of exon 18
ctggactgacaaaattcggagaagttttaattcataatgtatatttctatattcttttctcttcaa---agatcatcacta-atctttttctgctaaatttcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
| | |||| | || ||| || | || | ||| | | | || || || | | | ||| |||||| | | || |||||||| | | || || || ||||| | || |||||||| || ||||| || ||||||||||||| ||||||||||||||||| || | | |
actaccggttaaaactgtga----tttctttttctgctgcttgtttttctcctgcattttcaagaagctaaagttttactgtgcctttttatctcatcttgtagGTTTCTTTGCTGAACATAGTTGTGGAGCTCAAAAAGTGCTGTAATCATCCATTTCTGTTTGAAAGTGCCGACCATGGCTATGGTGGAGATGCGAACATGA
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S317_10V6.1 (Physcomitrella patens), 3'ss of exon 18
ctggactgacaaaattcggagaagttttaattcataatgtatatttctatattcttttctcttcaa--agatcatcactaatctttttctgctaaatttcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
| ||| | | | | || | | | || || | | || | || || | |||| | | | | | | |||||||| | || || || || ||||| | ||||||||||| || ||||| ||| ||||||||||||| ||| ||||||||||||| || || | |
--gatttgaaatcgtcatgtattctcttgcaacctgctttacccttgtgttttttacgagctcaaattaagtcatattgcagttgtgtgtttcattgcccagGTTTCCTTATTGAACATAGTCGTGGAGCTCAAGAAGTGCTGTAATCATCCATTCCTGTTTGAAAGTGCCGACTATGGCTATGGTGGAGATGCAAACACAA
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 17
lower sequence: EFJ28029 (Selaginella moellendorffii), 3'ss of exon 16
ctggactgacaaaattcggagaagttttaattcataatgtatatttctatattcttttctcttcaaagatcatcactaatctttttctgctaaatttcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
|||| ||| | | ||||| || || | | | || || ||| || ||||| ||||| | || || || |||||| ||||||||||||||||||||||||| | ||||| ||||| || ||||| || || | | || | |
--------------------------------------gtatttttttgcgtcctttttcttt---------tcgc-atttttgaactcctaccttgcagGTGTCTCTGCTGAACATAGTTGTGGAACTAAAGAAGTGCTGCAACCATCCCTTTCTTTTTGAGAGTGCGGATCATGGTTACGGAGCAAATGCAACTATGA
upper sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 17
lower sequence: EFJ29460 (Selaginella moellendorffii), 3'ss of exon 16
ctggactgacaaaattcggagaagttttaattcataatgtatatttctatattcttttctcttcaaagatcatcactaatctttttctgctaaatttcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
|||| ||| | | ||||| || || | | | || || ||| || ||||| ||||| | || || || |||||||||||||||||||||||||||||||| | ||||| ||||| || ||||| || || | | || | |
--------------------------------------gtatttttttgcgtcctttttcttt---------tcgc-atttttgaactcctaccttgcagGTGTCTCTCCTGAACATAGTTGTGGAATTAAAGAAGTGCTGCAACCATCCCTTTCTTTTTGAGAGTGCGGATCATGGTTACGGAGCAAATGCAACTATGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctatattcttttctcttcaaagatcatcactaatctttttctgctaaatttcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
tgctaaa putative branch site (score: 2)
tctttttctgct CT-rich tract
taatcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctggactgacaaaattcggagaagttttaattcataatgtatatttctatattcttttctcttcaaagatcatcactaatctttttctgctaaatttcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - actgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctgc