Sequence
atgc intronic sequence ATGC exonic sequence...ttagtctccctgcattcatatgtctgtaaaatgttatatgcaccataccgaatattttttttttaaatttatttatgtgatttaatttcatcctggatagGATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGCGAAGCTGTAGGCCCTGAACCTACCAG
Basic information
species | Glycine max |
transcript | GLYMA20G24790.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------ttagtctccctgcattcatatgtctgtaaaatgttat-atgcaccataccgaa--tattttttttttaaatttatttatgtgat---ttaatttc----atcc--tggatagGATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGCGAAGCTGTAGGCCCTGAACCTACCAG
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gtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaatagGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG
upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------------------------------------------ttagtctccctgcattcatat-gtctgtaaaatgttatatgcaccataccgaatattttttttttaaatttatttatgtgatttaatttcatcctggatagGATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGCGAAGCTGTAGGCCCTGAACCTACCAG
| | | || | || | | || || || ||| | || || | || | || |||||| ||| | |||| ||||||| |||||||||||||| || ||||| ||||||||| ||||||| || || |||||||| || ||||||| || ||
gtatatcttacacacttttggtggcttaataaatgttgggagaaaagataaagttgtcaatactaattctcgtaaaaattactagagtaagatttccataagatctgctactagacaataatttcatgtgcttaagtttcagcacactaccatacatggttaatgatttcaattgcttatgt--tttcttaacatctc----agGATAAATCTTGGCGTGTGCGCTATATGGTGGCAAATCAACTGTATGAACTATGTGAAGCTGTTGGTACTGAACCCACAAG
upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 4
ttagtctccctgcattcatatgtctgtaaaatgttat--atgcaccataccgaatattttt----------tttttaaatttatttatgtgatttaatttcatcctgga-tagGATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGCGAAGCTGTAGGCCCTGAACCTACCAG
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gtaaa-taaatgtgtgaatatgataaaaaaattctattgatgagctttatgggaaagctgtaaggcagatatgtatgagctgctttatcttgatttttttcgtctttgagcagGATAAGTCCTGGCGTGTGCGTTATATGGTTGCAAATCAGCTCTATGAACTTTGTGAAGCTGTAGGACCGGAGCCAACTAG
upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 3
ttagtctccctgcattcatatgtctgtaaaatgttatatgcaccataccgaatattttttttttaaatttatttatgtgatttaatttcatcctggatagGATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGCGAAGCTGTAGGCCCTGAACCTACCAG
| |||||||||| | |||| | || | ||| | | | ||| | || ||| ||| |||||||||||||||||||||| || ||||||||||||||| | || |||||||| ||||| || || ||||| ||||| ||
-------------gtgattatgtctgtaggcttttatgctgat-------gatctacatttaaaagaaatgcttaatctttgtactttttcactgagcagGATAAGTCTTGGCGTGTGCGCTATATGGTTGCAAATCAACTCTACGAGCTTTGTGAAGCCGTGGGACCTGAGCCTACTAG
upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 3
-ttagtctccctgcattcatatgtctgtaaaatgttatatgcaccataccgaatattttttttttaaatttatttatgtgatttaatttcatcctg--gatagGATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGCGAAGCTGTAGGCCCTGAACCTACCAG
| | | || || | | | || | || | | ||| || ||||| || ||| | ||| | ||| |||| || || | |||| | ||||||||||| || |||||||||||| ||||||| ||||||||||| | |||||||| |||||| |||||||
ttaaacaaatcaatatcgatg-atattcaggtcattcattacatc-ttccgtctactttttactttt-tttttatatatatttttattttattgtgtgaacagGACAGATCTTGGCGTGTTCGCTACATGGTTGCAGATCAATTATATGAGCTTTGTCATGCTGTAGGGCCTGAAGCTACCAGMapped 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|6501968|gb|AW203341.1|AW203341EST: CACAAGATTGTGTTGCACATATACTCCCGGTTATTGTTAACTTCTCCCAG GATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTT
genomic: CACAAGATTGTGTTGCACATATACTCCCGGTTATTGTTAACTTCTCCCAGgtacatgata ... tcctggatagGATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTT
EST:
gi|15203829|gb|BI426597.1|BI426597EST: CACAAGATTGTGTTGCACATATACTCCCGGTTATTGTTAACTTCTCCCAG GATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTT
genomic: CACAAGATTGTGTTGCACATATACTCCCGGTTATTGTTAACTTCTCCCAGgtacatgata ... tcctggatagGATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taccgaatattttttttttaaatttatttatgtgatttaatttcatcctggatagGATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGCGAAGCTGTAGGCCCTGAACCTACCAG
atttaat putative branch site (score: 4)
tttcatcct CT-rich tract
aatattttttttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagtctccctgcattcatatgtctgtaaaatgttatatgcaccataccgaatattttttttttaaatttatttatgtgatttaatttcatcctggatagGATAAGTCTTGGCGTGTGCGTTACATGGTTGCAAATCAATTGTATGAGCTTTGCGAAGCTGTAGGCCCTGAACCTACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - tctccct
- - - - - -gcattca
- - - - - - - - - -atgtctg
- - - - - - - - - - - - - - - - - tatatgc
- - - - - - - - - - - - - - - - - - - - - ccatacc