Sequence
atgc intronic sequence ATGC exonic sequencegtttgtctcaacttctcaagtaataattatccctccctgacttattgttactgacataggatgtggaatgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
Basic information
species | Glycine max |
transcript | GLYMA07G37050.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
--------------------gtttgtctcaacttctcaagtaataat-tatccctccctgac--ttattgttactgacatagg-atgtggaatgat--agGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
||| | | |||| ||| ||| |||| | | | | | | ||| || || | | || |||| || |||| || |||||||| ||||| |||||||| | ||||| |||||||||||||||||||||||||| ||||
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 9
-----------------gtttgtctcaacttctcaagtaataattatccctccctgact--tattgttactgacataggatgtgg----aatgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
|| | || | || |||||| | || |||| || ||| | || |||| ||| | | ||||| || | ||||| || ||||| ||||| ||||| || | |||||||||||||||||||||||||| ||||| || |
gtatgttgaaacaaatgaattaccatgctttgttcag-aataatc--ctcttcctggcttgtatgggatctaacatgccatgcatttttatttgtagGTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTG
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
------------gtttgtctcaa-----cttctcaagtaataattatccctccctgacttat-tgttactgacataggatgtggaatgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
||| | || ||| | || || | | || | || || | | | | ||||| | | |||| || ||||||| || ||||| ||||| ||||||||| | |||||||| ||||||||||||||||||||||||||||
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
--------------------------gtttgtctcaacttctcaagtaataattatccctccctgactta---ttgttactgacataggatgtggaatgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
||| ||| ||| || ||| | | | | | ||| ||| | | | | || ||| |||| ||| ||||||| ||||| || ||||| ||||| ||| | |||||||||||||| ||||| ||||||||||| ||||
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatg-cagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtctcaacttctcaagtaataattatccctccctgac--ttat-tgttactgacataggatgtg------gaatgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
||| || |||| || |||| || | | |||| | || | | || || | |||||||| || || || ||||| || |||||||| ||||| || |||||||||||||||| || ||||| ||||||||||| |
gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtctcaacttctcaagtaataattatccctccctg-acttattgttactgacatagg--atgtgga---atgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
|| || | | | | | | || ||| | | | | || || || | | || | | |||||||| || | || ||||| ||||||||||| ||||| || |||||||||| ||||| |||||||| ||||||||||| |
gtcggttttatttgcatatacataccttttccttgtcagcaattctttctatatgctaaattcatttctacttgtgatagGTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTG
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------gtttgtctcaacttctcaagtaata-attatccctccctgacttattgttactgacataggatgtggaatgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
|| | | ||| | || | | | | | | | | | | | || || | ||||| || ||||| ||||| || ||||||||||||||||||||||||||||||||||| || || || ||||| ||||| |
gtaagcgatcttcgtctctttatgattcaccacttatgtaaccttagttatatggtatttttcgtgacaatctggtttgcgtgagagtaaacgacgtaatttgggcaccgtgtttagaatattaactcaaatggctcttggtgacggtgttctagGTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTG
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------------------------------------------gtttgtctcaacttctcaagtaataattatccct-------ccctgactta----ttgttactgacataggatgtggaatgat-----agGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
||| ||| || | | || || || | || || | |||| | | | || || || | | | |||| || || || || || || || |||||||||||||||||||||||||||||||| || || || ||||| ||||| |
gtgagtagcctcctacttgtggtcctctactgagtctatcttggatgctacttttgatgttgatctgaattgcgtgagagtgaacgatgtcaatgggcgttttgtctcagaagttgtaattatcttatcatttgtagcggtggtgcagGTACCACACTTGTATTGCATCGGCGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCTCAAGGCATTTCGG
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
gtttgtctcaacttctcaagtaataattatccctccctgacttattgttactgacataggatgtggaatgat--agGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
| || || |||| ||||| |||| | || || | |||| |||||||| ||||| || || |||||||||||||| ||||||||||||| ||||||||||| || || |||||||
---------------------gttggttgtcttcgtttgacaa---gttacatacatgacttttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
upper sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 9
gtttgtctcaacttctcaagtaataattatccctccctgacttattgttactgacataggatgtggaatgat--agGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
| || | |||| ||||| |||| || || | |||| |||||||| ||||| || || |||||||||||||| ||||||||||||| ||||||||||| || || |||||||
---------------------gttggttgttttcgtttgacaa---gttacatacatgactcttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaataattatccctccctgacttattgttactgacataggatgtggaatgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
tactgac putative branch site (score: 1)
ttattgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtctcaacttctcaagtaataattatccctccctgacttattgttactgacataggatgtggaatgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA