Sequence
atgc intronic sequence ATGC exonic sequencegtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
Basic information
species | Glycine max |
transcript | GLYMA07G26540.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g50320.1 (Oryza sativa), 3'ss of exon 9
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
||| | | | | || | ||||| |||| | | | | | || | | ||||||| || || | | || |||||||| ||||| |||||||||||||| ||||| || |||||||| ||||| || |||||||| | || |||||||||||||||||||| || |||||||
gtatggcactagaattcctgtttattatggatttaat----gggaccaatgctgtgggtcat-gcctttgctaactgcctc---------ttgttta-cagATGTTGGCAAAAAAGGTAGATACATTAACCAAGGCTATGGAAGTGGAGGCTAAAAAGATGAGGCGAGAGGTAGCTGCTATGGAGAAGGAAGTTGCTGCTA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G039325_T01 (Zea mays), 3'ss of exon 9
gtaaatgtttg-gtctatttattgtatttggatataatccttgacttcttattta-taaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
|| || ||| |||| || | || | | || | || ||||| | | || || | | | | ||| ||||||||||||||||| ||||| || || |||||||| |||||||| ||||| | ||| | ||| | || || || || |||||||| || || || || |
------gtatgcgtccatttctt-tccttattcgttcactttagtggatagttagctaaatactgattattatgaagtttgcttatctattgttgtctggcagATGTTAGCAAAGAAAGTAGACACCTTAACCAAAGCAATGGAAGTGGAGGCTAGAAAGGTCAGACGAGAGGTTGCAGCCATGGAGAAAGAAGTTGCAGCAA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaatgtttggtctattta--ttgtatttggatataatccttgacttcttatttataaatgatagtccttgct--aattgtttccaatggccat-catctat-----cagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
|||| ||| || | |||| || | ||| ||| | | | ||| |||| | | || | |||| | || | | | || | | || ||||| |||| |||||||| || ||||| || || || ||||| ||||| ||||||||||||||| ||||||||||||| ||||| || || || ||||| |
gtaagagttctgtttctttaagttctgtttctttatgccatattaat-cttgtttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgtagATGCTAGCGAAGAAGGTGGAAACATTAACAAAGGCAATGGAGGTTGAAGCAAAGAAGATGAGACGGGAAGTAGCTGCAATGGAAAAAGAAGTTGCTGCAA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
|| | | || || |||| ||| | || ||| | ||||||| || || || | || | || | | | | | ||||||| || |||||||| || ||| | || || || |||||||| || |||||||||||| |||| |||||||| || |||||||| ||||| | ||||
gttagtcattagt---tttac-acctttccaagaaacgtttg--cttatatttatttat-attctctgatcaaaatacttgggcttgtgtttgctt-ttagATGTTGGCCAAGAAGGTTGAAACACTAACAAAGGCGATGGAAGTGGAAGCAAAGAAGATGCGAAGAGAAGTAGCAGCAATGGAGAAAGAGGTTTCAGCTA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttcca-atggccatcatctatc-agATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
||||| ||| | ||| || | | ||| | | | | ||| || | || ||| | | | |||| | ||| ||||||| || |||||||| || ||||| || || || ||||| |||||||||||||||||| |||| |||||||||| |||| ||| || || ||||| |
------gtttg--ctagtgtttggccttttttcctgttctttgccgcctttatatgaaatgttgtataatataagtctaaagatatgggttgtgtatatttagATGTTGGCCAAGAAGGTTGAAACATTAACAAAGGCGATGGACGTTGAGGCAAAGAAGATGCGAAGAGAAGTAGCTGTAATGGGGAAAGAAGTTGCTGCAA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
| | | | | || || || | | | || || | || | || | | || | || | ||| ||||||||||||| ||||| || || || || || || ||||||||||| ||||||||||||||||||||||| ||||| |||||||| ||||| ||||| |
---------------gtaaaatctctctgaatgtaccatataaaatgttgttaaaaagacgt-gtttgtaatggaagtct----tgatatttttcttgtagATGTTAGCAAAAAAGGTTGAAACTTTAACAAAGGCAATGGAAGTTGAAGCAAAGAAGATGAGAAGGGAAGTGGCTGCAATGGAGAAAGAGGTTGCTGCAA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 9
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
|| | | ||| | || ||| | || | ||| | ||||| || || | | || | | ||||||| |||| ||||||||||||||||| ||||| || |||||||||||||| |||||||||||||||||||| ||||| |||||||||||||||||||| |
----------------gttggtattcttgtcctca---tctgtcttatgatgctttaattcatatttttgctcat-gtatttggatgtaattctttttcagATGCTAGCTAAGAAGGTAGATACATTAACCAAGGCAATGGAAGTTGAGGCTAAGAAGATGAGAAGGGAAGTTGCTGCCATGGAGAAGGAGGTAGCTGCCA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S136_188V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------------gtaaatgtttggtctatttattgtatttggatataatcctt--gacttcttatttataaatgatagtc-------cttgctaattgtttccaatg-gccatcatctat-cagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
|| | | | | |||||| || | | | | | || | ||| | | || || ||| | || ||| |||| | | || | | |||||| | ||||||| || || || || | || || |||||||||||| ||||||||||||||| ||||| || ||||||||||| || || |
gtgcgtatagggtaaactacatcttactagcatatgaatacttctctgcttagtgagttttgcattgatttttgaacaacttgattatatttatcgactgcagatattgttgttacctcgtaccttcccggtttgctgtttttgacatgtattcacgctggcttcgtggctgcttctaatgtgttctgatatgtgcagATGCTCTCAAAGAAAGTCGACACTTTATCTAAGGCTTTGGAAGTTGAGGGAAAGAAGATGAGAAGAGAAGTCCAAGCAATGGAGAAGGAAGTTGCCACCC
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 9
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
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---------------------------------------------gtatatgcgtgggtt-tggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAGCAATGGAGAAGGAGGTGGCCGCGA
upper sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ36655 (Selaginella moellendorffii), 3'ss of exon 9
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
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---------------------------------------------gtatatgcgtgggtt-tggctctaggtgctcatgacagtcggacttttgcatgcagATGCTGTCCAAGAAGGTGGATACGCTGACCAAGGCAATGGAAGTAGAGGCGAAGAAGATGCGTAGGGAGGTAGCAACAATGGAGAAGGAGGTGGCCGCGAMapped 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|7042614|gb|AW472508.1|AW472508EST: CTGGTCATGAGAAAGATCAAAGCCTAAAAGATAAAGGCGATGCTATTGAG ATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
genomic: CTGGTCATGAGAAAGATCAAAGCCTAAAAGATAAAGGCGATGCTATTGAGgtaaatgttt ... catctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
EST:
gi|6747727|gb|AW318183.1|AW318183EST: CTGGTCATGAGAAAGATCAAAGCCTAAAAGATAAAGGCGATGCTATTGAG ATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
genomic: CTGGTCATGAGAAAGATCAAAGCCTAAAAGATAAAGGCGATGCTATTGAGgtaaatgttt ... catctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
tgctaat putative branch site (score: 2)
ttataaatgatagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatgatagtccttgctaattgtttccaatggccatcatctatcagATGTTAGCAAAGAAGGTAGATACATTGACCAAAGCCATGGAAGTTGAGGCAAAGAAGATGAGAAGGGAAGTAGCTGCTATGGAGAAGGAGGTAGCTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT