Sequence
atgc intronic sequence ATGC exonic sequencegttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
Basic information
species | Glycine max |
transcript | GLYMA08G05100.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagcta-attgttgc--aatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
|||| | || | || || | ||||| | || | || | | | | |||| | || | || | | |||||| ||||||| || ||||||||||| ||||| || |||||||| ||||| || |||||||| |||| |||||| | ||||||||||| || ||||| |
----gtatggcactagaattcc-tgtttattatggattt---aatgggaccaatgctgtgggtcatgcctttgctaactgcctcttgttta-cagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 9
gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
|||| | || ||| |||| | | | || | | | || |||| |||| | || || || |||||||| || |||||||||||||| || || ||||| |||||||| ||||| || || ||||| | || || ||| |||||||||| || || || || |
----gtatggaaatatt-ttgcttatttgttgcactgagttcataggaagct-cgatattagaaaatttacctgtttcttcttgtcctacagATGCTTGCTAAGAAAGTAGATACCTTAACTAAAGCTATGGAAGTAGAGGCGAAAAAAATGAGGCGGGAGGTTGCTGCCATGGAGAAAGAAGTTGCAGCTA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 5
gttagtattt-ttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
|| || | | ||| ||| | || | | | ||| ||| || |||| | | ||| || | | |||||| ||||||||||||||||||| ||||| ||||| ||||| || || ||||| ||| | || ||||| | |||||||||||| | || ||
gtaaggactagccttgagactggctcgctgtcct----cttcatttgtctattgcttcctcg--taat-gaagtgatg--tgctgta---cagATGTTGGCAAAGAAAGTAGATACTTTGACAAAAGCTATGGAGTCAGATGCCAAGAAATCGAGGCGCGAGCTAGCTGCTATGGAGAAGGAGCTGGCAGCTG
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G039325_T01 (Zea mays), 3'ss of exon 9
--gttagtatttttttgttcttggatattaatctta---gatttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
| || ||| | | ||| || | ||| ||| || | | | | | | ||| | || | ||||| |||| |||||| | |||||||||||||| || || |||||||| |||||||| ||||| | ||| | ||| |||| || || |||||||||| || || || ||||
gtatgcgtccatttctttccttattcgttcactttagtggatagttagctaaatactg-attattatgaagtttgcttatctattgttgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCTAGAAAGGTCAGACGAGAGGTTGCAGCCATGGAGAAAGAAGTTGCAGCAA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G832989_T02 (Zea mays), 3'ss of exon 9
-------gttagtatttttttgttcttgg-ata-ttaatcttagatttcta-attgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
||||||| || | | ||| | || || || | | || | | | | || || | |||| || |||||||| |||||||||||||||||||| ||||| | |||||| ||||| || |||| ||| ||| ||||| | ||||||| | | || ||
gttcaaaactagtattgaattagattggacatagtggatattgtatgtgaggaaacatgactgtggttcta-tggtttagcttatcaactgttgccta-cagATGCTAGCAAAGAAAGTAGATACATTACATAAAGCAAAGGAAGTGGAGGCTAAAAAGAAGAGGCAAGAGATAGCTGCTTTGGAGAAAAAATTTGCCGCGG
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------------gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatg----gttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
| ||| | ||| || | ||||||||||| ||| | || ||| | | || | | |||| |||| | | || ||||||| || ||||| || || ||||| || || || ||||| ||||| ||||||||||||||| | ||||||||| | ||||| || || || |||||||
gtaagagttctgtttctttaagttctgtttctttatgccatattaatcttg--tttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgt-agATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 10
gttagtattt--ttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
|||||| || |||| | | | || | | || || || | || || ||| | | || | | |||| || | ||||| |||| ||||| || || ||| | || || || |||||||| || |||||||||||| ||||||||||||| | |||||||| ||||| | || |
gttagtcattagttttacacctttccaagaaacgtttgcttatatttatttat-attctctgatcaaaatacttgggcttgtgtttgcttttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 9
gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgt---cagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
||| | | |||| ||| | | |||| | || | || | | | | | ||| | | || ||| | | | ||||| |||| ||||| || || ||||| || || || ||||| |||||||||||||||||| |||||||||||||| |||| ||| || || |||||||
gtttgctagtgtttggccttttttcctgttctttgccgcctttatatgaaatgttgtataatataagtctaaagatatgggttgtgtatatttagATGTTGGCCAAGAAGGTTGAAACATTAACAAAGGCGATGGACGTTGAGGCAAAGAAGATGCGAAGAGAAGTAGCTGTAATGGGGAAAGAAGTTGCTGCAA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 9
gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
| | | || || | || | | ||| ||| | | | |||| | | || | || ||| ||||| | ||||| || || || || || || || || ||||||||||| ||||||||||||||||| ||||| ||| | |||||||| ||||| |||||||
-------gtaaaatctctctgaatgtaccatataaaat----gttgttaaaaagacgtgtttgtaatggaagtcttgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 9
gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
||| ||||| || | || || ||||| | || || || | ||| | || | | || ||| | || | | ||||||||| || ||||| ||||||||||| ||||| || |||||||||||||| |||||||||||||| ||||| ||| |||||||||||||||||||||| |
gttggtattcttgtcctc------atctgtcttatgatgct--ttaat--tcatatttttgctcatgtatttggatg-taattctttttcagATGCTAGCTAAGAAGGTAGATACATTAACCAAGGCAATGGAAGTTGAGGCTAAGAAGATGAGAAGGGAAGTTGCTGCCATGGAGAAGGAGGTAGCTGCCA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S136_188V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------------------------------------------------------------------gttagtatttttttgttcttggatatt---aatcttagatttctaattgataattataat--cttagctaattgttgcaatg-gttgttatctgt-cagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
| |||| || | || | | || | | ||| | | || | | | ||| | | || |||| ||| | || ||| |||||||| |||||||||| || || || | || || |||||||||||| ||||||||||||||||||||| | ||||||||||| || || |
gtgcgtatagggtaaactacatcttactagcatatgaatacttctctgcttagtgagttttgcattgatttttgaacaacttgattatatttatcgactgcagatattgttgttacctcgtaccttcccggtttgctgtttttgacatgtattcacgctggcttcgtggctgcttctaatgtgttctgatatgtgcagATGCTCTCAAAGAAAGTCGACACTTTATCTAAGGCTTTGGAAGTTGAGGGAAAGAAGATGAGAAGAGAAGTCCAAGCAATGGAGAAGGAAGTTGCCACCC
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgt-cagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
|| | | | ||| | | | || | | || | | ||||||||| | ||||| || ||||| ||||||| || |||||||| ||||| ||||||||| | || || ||||| | |||||||||||||| || || |
--------------------------------------gtatatgcgtgggtttggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
upper sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ36655 (Selaginella moellendorffii), 3'ss of exon 9
gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgt-cagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
|| | | | ||| | | | || | | || | | ||||||||| | ||||| || ||||| ||||||| || |||||||| ||||| ||||||||| | || || ||||| | |||||||||||||| || || |
--------------------------------------gtatatgcgtgggtttggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAACAATGGAGAAGGAGGTGGCCGCGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|207837165|gb|GD808810.1|GD808810EST: TTGGTCATGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCCATTGAA ATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
genomic: TTGGTCATGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCCATTGAAgttagtattt ... tatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
ataattataatcttag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcagATGCTGGCAAAGAAAGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGAGAAGTAGCTTCCATGGAGAAGGAGGTAGCTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC