Sequence
atgc intronic sequence ATGC exonic sequence...gctttgttacgataaagcccacgactgaattagagttttaataatatttaattatttgtcatatattactttttaaaactctattgtgcaatcatgatagCCGTGCCTCTGATTTTGGTCTAATGAAGATAGACAATAAAGGAAGGGTCCTTTCGTTTAGTGAAAAACCCAAAGGAGAAGAGCTGAAAGCAATG
Basic information
species | Glycine max |
transcript | GLYMA07G38820.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------------gctttgttac-gataaagcccacgactgaattagagttttaataatatttaattatttgtcatatattactttttaaaactctattgtgcaatcat-gatagCCGTGCCTCTGATTTTGGTCTAATGAAGATAGACAATAAAGGAAGGGTCCTTTCGTTTAGTGAAAAACCCAAAGGAGAAGAGCTGAAAGCAATG
| ||| |||||| | | ||| | || | ||||||| | || ||| | |||| | | | | || | || | | ||||| || ||||||||||||||||||||||||||| | | |||||| || | | |||||||||||||| |||||||| || | || ||||||
gtgattcctgtaccatttcagtagcttcatccatgaacaatgaagtgacctctcataccaagttttagataaattgaattgttttatttg-gtaagagaaatatttggattttgaaaatacactactctctttcatttgtttatttcgtccttgtcagCCGGGCATCTGATTTTGGTCTAATGAAGATAGACGACACAGGAAGAGTTATCGCATTTAGTGAAAAACCAAAAGGAGATGATTTAAAGGCAATG
upper sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 2
gctttgttacgataaagcccacgactgaattagagttttaataatatttaat--tatttgtcatatattactttttaaaactctattgtgcaatcatgatagCCGTGCCTCTGATTTTGGTCTAATGAAGATAGACAATAAAGGAAGGGTCCTTTCGTTTAGTGAAAAACCCAAAGGAGAAGAGCTGAAAGCAATG
| | | || | | | | || | | ||| | | | | | | | | | | | || | ||| ||||| || ||||||||||| ||||||||||||||| | | |||||||| |||| || ||||| ||||| |||||||| || | || ||||||
tttgagcatccgctaaactctc--tttcatgtatttccataccccgtttggtcctggtctccttgtggatttgatcatgaatgagtttcttttttatgtcagCCGGGCATCTGATTTTGGCCTAATGAAGATAGACGACACTGGAAGGGTAATTTCATTCAGTGAGAAACCAAAAGGAGACGAATTAAAGGCAATG
upper sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 6
gctttgttacgataaagcccacgactgaattagagttt-taataatatttaattatttgtcatatattac---tttttaaaactctattgtgcaatcatgatagCCGTGCCTCTGATTTTGGTCTAATGAAGATAGACAATAAAGGAAGGGTCCTTTCGTTTAGTGAAAAACCCAAAGGAGAAGAGCTGAAAGCAATG
| | | | | || | | || ||| || | | || | ||| | || | || ||| | || | |||| ||| |||||||| |||||||| || ||||||||||| | |||||||| || | || || ||||||||||| |||||||| || ||||||||||||
--gtgaatgcaaaagagtatatagatcctttcatttttaccccaacttatcatactgaatcaaagatcatgatttcttatagtctctttctatttacatggtagACGTGCCTCAGATTTTGGGCTTATGAAGATAGATGACAAAGGAAGAGTTATCTCATTCAGTGAAAAACCTAAAGGAGACGACCTGAAAGCAATG
upper sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------gctttgt-tacgataaagcccacgactgaattagagttttaata-----atatttaattatttg-tcatatattactttttaaaactctattgtgcaatc-atgatagCCGTGCCTCTGATTTTGGTCTAATGAAGATAGACAATAAAGGAAGGGTCCTTTCGTTTAGTGAAAAACCCAAAGGAGAAGAGCTGAAAGCAATG
|| | | | | || | | | | |||| | || || | || ||| || | | | ||| ||| | ||| | | || ||||||||||||| || ||||| ||| |||||||||||||||| ||||||||||| || | || |||||||| || ||||||||||| |||| ||||||
gtaggttctatttcctatactggtttcaactctttatgctattagccaaatgcctgagcctctttgttcatgtccctgttttcctttagatgattgaaaactacccttttgagttctttctctctttccatgatagCCGTGCTTCAGATTTCGGTTTAATGAAGATAGACAACAAAGGAAGGGTTCTCTTCTTCAGTGAAAAGCCTAAAGGAGAAGATTTGAAGGCAATGMapped 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|151404121|gb|EV273931.1|EV273931EST: CGGGAGAGTGGTGCAGATATCACTCTTTCTTGTCTTCCAATGGATGACAG CCGTGCCTCTGATTTTGGTCTAATGAAGATAGA
genomic: CGGGAGAGTGGTGCAGATATCACTCTTTCTTGTCTTCCAATGGATGACAGgtaggttgct ... atcatgatagCCGTGCCTCTGATTTTGGTCTAATGAAGATAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttaattatttgtcatatattactttttaaaactctattgtgcaatcatgatagCCGTGCCTCTGATTTTGGTCTAATGAAGATAGACAATAAAGGAAGGGTCCTTTCGTTTAGTGAAAAACCCAAAGGAGAAGAGCTGAAAGCAATG
atttaat putative branch site (score: 4)
attatttgtcatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctttgttacgataaagcccacgactgaattagagttttaataatatttaattatttgtcatatattactttttaaaactctattgtgcaatcatgatagCCGTGCCTCTGATTTTGGTCTAATGAAGATAGACAATAAAGGAAGGGTCCTTTCGTTTAGTGAAAAACCCAAAGGAGAAGAGCTGAAAGCAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - -agcccac
- - - - - - - - - - - gactgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attgtgc