Sequence
atgc intronic sequence ATGC exonic sequence...ttatattaataaatatcccatcttcattgtgtattagatagataattcataatagtctttaagacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTGGCCATAAGCGTGGTGAGAAGTTTGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCTAATGATA
Basic information
species | Glycine max |
transcript | GLYMA02G01930.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 3
---ttatattaataaatatcccatcttcattgtg-tattagatagataattcataatagtctttaagacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTGGCCATAAGCGTGGTGAGAAGTTTGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCTAATGATA
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attttatcatgtttaat-tctcatgttaacattactgtgagctaagtttgtgttattatactgtaatatcttaccatttctgatctgcttttgcaattt---agGTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAGTTTGTACACCCTAATGATCATGTGAACAGATCACAGTCCTCAAATGATA
upper sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 3
ttatattaataaatatcccatcttcattgtgtattagatagataattcataatagtctttaagacttgagaatccattttcttttttctgatctt--ttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTGGCCATAAGCGTGGTGAGAAGTTTGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCTAATGATA
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tagttttcctgta-agctaatgttcat-gtgaattttattgtgaacctatcatgcttctgccaactgtgctatattgtttatgatctcttttccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA
upper sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G348729_T01 (Zea mays), 3'ss of exon 6
ttatattaataaatatcccatcttcattgtgtattagatagataattcataatagtctttaagacttgagaatccattttcttttttctgatctt--ttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTGGCCATAAGCGTGGTGAGAAGTTTGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCTAATGATA
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tagttttcctgta-agctaatgttcat-gtgaattttattatgaacctagcatgtttctgccagctgtgctatattgtttatgatctcttttccgaattcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGGGCGGTCAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA
upper sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 4
---------ttatattaat--aaatatcccatcttcattgtgtattagatagataattc--ataatagtctttaagact-tgagaatccattttcttttt---------tctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTGGCCATAAGCGTGGTGAGAAGTTTGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCTAATGATA
|| | | | | | ||| | || | || |||| || | | | || |||| | | || | ||||||||||| | || |||| ||||| ||||| || ||||||| ||||||||||| | || ||||||||||| | ||||||||||||||||||||| || |||||||| |||||||| || |
gtaatttctttgcagtttttgagacatctgttgaggatctcattgtatatagctagctacaagagaaggctttctgtttatgttttttcattttcttttggccttgttatttgctcttcacagGTCATTGCTAATAGAGCAGCTGAGATTCTTGGTCGCAAACGTGGTGAGAAATGTGTGCACCCAAATGACCATGTGAACAGATCACAATCTTCTAACGACA
upper sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 2
ttata--ttaataaatatcccatcttcattgtgtattagatagataattcataatagtctttaagacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTGGCCATAAGCGTGGTGAGAAGTTTGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCTAATGATA
||| |||| | || || ||| ||| |||||| || | | | || | | | || | |||| | | | ||| ||||| ||||| || ||||||| ||||||||||| || || |||||||| || |||||||||||||||||||||| || |||||||| ||||||||||| |
ttaagagttaagactaattacaatgtcaaaaatgattttttagatacttaaccaccagacgtccgaggtaattaaacagatcattttgt--gctttttacagGTCATTGCCAATAGAGCAGCTGAGATTCTTGGTCACAAACGTGGTGAAAAAATTGTGCACCCAAATGACCATGTGAACAGATCACAATCTTCTAATGACA
upper sequence: GLYMA02G01930.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 4
-ttatattaataaatatcccatcttcattgtgtattagatagataattcataatagtctttaagacttgagaatccattttcttttttctgatctttt-cagGTTATTGCAAACCGAGCAGCAGAGATTCTTGGCCATAAGCGTGGTGAGAAGTTTGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCTAATGATA
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caggatttagtattctttgcctacgaactgtatacttgtcattt--ttggtgatgaatattacttctttttatttggatttattttttatcaactgtggcagGTTATTGCAAATAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATAMapped 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|19935949|gb|BQ080654.1|BQ080654EST: TTGTATGGCAAACTGGGAGTGGCACTCAAAGTAACATGAATGCTAACGAG GTTATTGCAAACCGAGCAGC
genomic: TTGTATGGCAAACTGGGAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagt ... atcttttcagGTTATTGCAAACCGAGCAGC
EST:
gi|19934370|gb|BQ079400.1|BQ079400EST: TTGTATGGCAAACTGGGAGTGGCACTCAAAGTAACATGAATGCTAACGAG GTTATTGCAAAC
genomic: TTGTATGGCAAACTGGGAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagt ... atcttttcagGTTATTGCAAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcataatagtctttaagacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTGGCCATAAGCGTGGTGAGAAGTTTGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCTAATGATA
ttctgat putative branch site (score: 3)
tccattttcttttttc CT-rich tract
attttcttttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatattaataaatatcccatcttcattgtgtattagatagataattcataatagtctttaagacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTGGCCATAAGCGTGGTGAGAAGTTTGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCTAATGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA