Sequence
atgc intronic sequence ATGC exonic sequence...gggggccgctacggccgctattgacaactatgatccctggtgaacatccctgtggggttctgcaatggcaaaattaacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
Basic information
species | Glycine max |
transcript | GLYMA10G25630.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 13
gggggccgctacggccgctattgacaactatgat-ccctggt--gaacatccctgtggggttctgcaatggcaaaattaacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
| | | | | || | | | | ||| | || | || ||| | || | || | || | | || ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||| ||||| |||||||| || || || |||||| |||
-acacacaatgatgttgagaatggaagttgaattgcactgctaggagtggtgccctgaagttatattttgacctgtatatgcatcatgac--ctttcctacagATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAG
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 13
gggggccgctacggccgctattgacaactatgatccctggtgaacatccctgtggggttctgcaatggcaaaattaacatttgaaa---ctg---cccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
| || ||||| || | || || |||| ||| || | || ||| || | ||| ||| ||| || | | || ||||||| ||||| |||||||| || |||||||||||||||||||||||||| ||||| ||||||| || || |||||||||||||| || |||||| |||
---agtggcggaacattctatt-actattactgattctagtgactgtcc-tgagttgtga-gcatgggtattatttttttttaaaaaaattggatctttcctttagATTGGTGGAGCTAGTGAAGCGGAGGTTGGTGAGAAGAAGGATAGAGTGACTGATGCACTAAATGCTACCAAAGCTGCTGTAGAGGAGGGTATTGTACCAG
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 12
---------------------------------gggggccgctacg-gccgctattgacaactatgatccctggtgaacatc-cctgtggggttctgcaatggcaaaatta---acatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
|| ||| | | || | | || | | | | ||||||| |||| || | ||| | | || |||| |||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||| | ||||| ||||| |||||||| || || ||||||||| |||
gtgaggttattgacctactgtatgtatttacgaatggtagattacatgttcttgttttatatcgtaattg-taataactgttacctgtggctctctgatatttcctgattttgtgcctatgtgtgcatcctttcctagATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAG
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
-----------------------------gggggccgctacggccgctattgacaactatgatccctggtga-ac--atccctgtggg-gttctgcaatggcaaaattaacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
||| | | | | | ||| | | || | || | || | |||||| || || || | || | || || || | | || ||||||| ||||| || ||||| ||||||||||||||||||||||||||||||||||| | ||||| ||||| |||||||| || || || |||||| |||
gtgagattactgacctttgtatgtttactaatggcagattccat-gtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcct--agATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
gggggccgctacggccgctattgacaactatgatccctggtgaacatccctgtggggttctgcaatggcaaaattaacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
| | | | | | | || | | | || || || || | || | || | | | ||||||||||||| ||||| | |||||| |||| ||||| |||||||| || ||||| ||||||| ||||| || || |||||||| || ||||| |||
-------gtaatgtacacctcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatgggtttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 11
gggggccgctacggccgctattgacaactatgatccctggtgaacatccctgtggggttctgcaatggcaaaat-taacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
| || | | | | | | || | ||| | | |||| | | || | | |||| | || | || | | ||||||||||||| |||||||||||||||||||||||||| || |||||||||||||| || ||||| ||||| || || || || || || ||| || |||
-------gttagtccatgttataatgttttgggagtcttagaatcatagcagcctggttgta-agtgtcttgttataacttctggagctaattgtgtttagATTGGAGGAGCAAGTGAAGCTGAAGTTGGTGAGAAGAAAGACAGAGTGACAGATGCTTTGAATGCCACTAAAGCAGCAGTTGAAGAGGGTATTTTACCAG
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 12
----------------------gggggccgctacggccgctattgacaactat-gatccctggtgaacatccctgtggggttctgcaatggcaaaattaacatttgaaac-------tgcccttct--------gcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
| | || | | ||| | ||| | | | | ||||| | || | ||| || | ||| || | | |||| |||||||||||||| ||||||| ||| ||| |||||||||| || | || || ||||| || ||||| || || || ||||| ||||| |||||||| | |
gtatatcagtcatcctaatttaaatagttgtctcgtttgacaatgaaatttattggcacactacaatagtgcctgtagcatttca-agccttaaactttaaattgtaagtgattttatttctttctttgtgcttacagATTGGAGGAGCTAGTGAAGTTGAGGTTAGTGAGAAGAAAGACCGTGTTACTGATGCATTGAATGCCACCAAAGCCGCTGTTGAGGAGGGCATTGTTCCTG
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ32351 (Selaginella moellendorffii), 3'ss of exon 11
gggggccgctacggccgctattgacaactatgatccctggtgaacatccctgtggggttctgcaatggcaaaattaacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
|| | || | || || || ||| ||| || | | |||||||||||| |||||||| ||||| ||||| ||||||||| | ||||| ||||| | ||||| || |||||||| || ||||| || || || |||
---------------------------------------gtatgtacacc-aaagacttttgtggcagcgtttttattattgtttcgcgcgcgagcgtagATTGGAGGAGGTAGTGAAGCGGAAGTCGGTGAAAAGAAGGATCGGGTGACCGATGCGCTGAATGCTACAAAGGCTGCAGTGGAGGAGGGAATCGTGCCAGMapped 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|23734596|gb|BU765533.1|BU765533EST: AGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCCGTGCTTAAG ATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACA
genomic: AGTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCCGTGCTTAAGgtatgcctac ... ccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACA
EST:
gi|193546035|gb|FK504388.1|FK504388EST: GTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCCGTGCTTAAG ATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACA
genomic: GTTACAGGAAAGATTAGCCAAGCTTTCTGGTGGTGTTGCCGTGCTTAAGgtatgcctac ... ccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atccctgtggggttctgcaatggcaaaattaacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
aattaac putative branch site (score: 2)
ctgcccttct putative PPT
aaaattaacatttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gggggccgctacggccgctattgacaactatgatccctggtgaacatccctgtggggttctgcaatggcaaaattaacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - -ccgctac
- - - - - - - - gctattg
- - - - - - - - - - - - - - - - - -cctggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - tggggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactgc