Sequence
atgc intronic sequence ATGC exonic sequence...agcaacaatggaactatagaactattatttaagatcttaagtttgatataatttctaattaaagatgctgatctgaagtcatctcttaatttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
Basic information
species | Glycine max |
transcript | GLYMA20G02500.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g52479.3 (Oryza sativa), 3'ss of exon 1
---agcaacaatggaactatagaactattatttaagatcttaagtttgatataatttctaattaaagatgctgatctgaagtcatctc-ttaatttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
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tcttgaggtgcggaaacttaatctccattgttgtttgaatttggtttgggacggt--ctaagtttttctgctaaatctt--tcacttagttggatcattaacagGGTCCAGGAGGTGTTTGGTGTGATGTTGATGTTGTTGAATTTTCGTACTACGGTGCACCGGCTCAAACACCTAAAGAGCAAATGTTCAGTGAGCTTGTTG
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g31470.1 (Oryza sativa), 3'ss of exon 2
agcaacaatggaactatagaactattatttaagatcttaagtttgatataatttctaa-ttaaagatgctgatctgaagtcatctcttaatttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
||| | |||| | || | || | | | | | | | | || | | | | | |||| ||||| || || ||||||||||| |||||||| || ||||| || ||||| ||||| |||| |||||| || |||||||| ||| ||||||| ||
------------------------gtatacggatcatgtggtttagcaatatatttaggtcatatgcaattacataatga-atttactgtgtcatacatagGGACCGGGGGGAGTGTGGTGTGATGTCGATGTTGTTGAATTCTCTTACTATGGGGCACCAGCACCAACTCCAAAGGAACAATTGTATGACGAGCTTGTTG
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150212_T03 (Zea mays), 3'ss of exon 4
agcaacaatggaactatagaactattatttaagatcttaagtttgatataatt-tctaattaaagatgctgatctgaagtcatctcttaatttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
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-----------------gtaggcacgattttgtttcatgtagtttacaaagttatttaagccatctgaatcacatacagtttcgttgcattccataaacagGGACCTGGGGGTGTGTGGTGTGATGTTGATGTTGTTGAATTTTCTTATTATGGTGCACCAGCCCCAACACCGAAGGAACAACTTTATGATGAGCTTGTTG
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G078541_T01 (Zea mays), 3'ss of exon 3
-agcaacaatggaactatagaactattatttaagatcttaagtttgatataatttctaattaaagatgctgat-ctgaagtcatctcttaatttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
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tgatttcaatctctaattagagttttgacgtttaaacgtagtttaaacatcgtttaaacgtagttttaataacactgatttcatcgcgt--tccataaacagGGACCTGGGGGTGTGTGGTGTGATGTTGATGTTGTTGAATTTTCTTATTATGGTGCACCAGCCCCAACACCAAAGGAACAACTTTATGATGAGCTTGTTG
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G102346_T01 (Zea mays), 3'ss of exon 2
---------------------------------------agcaacaatggaactatagaactattatt-taagatcttaagtttgatataatttctaattaaagatgctgatctgaagtcatctc-ttaatttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
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gtaggggaactgtaattagtatgtattttggatgatcgggttagccatgctcccaaacaacaatgctggtgaagttttgtactttgaaaatcttttcgtcgtggt--ctgaatagctatcacttagtcggatcattgacagGGTCCAGGAGGTATTTGGTGTGATGTTGACGTTGTTGAGTTCTCGTACTACGGTGCACCAGCTCAAAATCCAAAAGTGCAAATGTTCACTGAGCTTGTTG
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G033724_T01 (Zea mays), 3'ss of exon 1
---agcaacaatggaactatagaactattatttaagatcttaagtttgatataatttctaattaaagatgctgatctgaagtcatctcttaatttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
| ||| | | | || | || | ||| | | | |||| || ||| | | | | ||| | | | | | |||||| || |||||| ||||||||||||| |||||||| ||||| || || || ||||| || || |||||||| |||| ||| ||| || ||||| | |
tgggttagttatgctcccaaacaa-tgctactgaagttttgtactttggaattctttttgcc--atggtctggatatttatcacttagtcggatcattgacagGGTCCAGGAGGTATTTGGTGTGATGTTGATGTTGTTGAGTTTTCGTACTACGGTGCTCCAGCTCAAACTCCAAAAGTGCAAATATTCACAGAGCTCGTGG
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G033724_T02 (Zea mays), 3'ss of exon 2
---------------------------------------agcaacaatggaactatagaactattatttaagatcttaagtttgatataatttctaattaaagatgctgatctgaagtcatctcttaatttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
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gtagggaagctgtaattcatacgtattttagatgattgggttagttatgctcccaaacaa-tgctactgaagttttgtactttggaattctttttgcc--atggtctggatatttatcacttagtcggatcattgacagGGTCCAGGAGGTATTTGGTGTGATGTTGATGTTGTTGAGTTTTCGTACTACGGTGCTCCAGCTCAAACTCCAAAAGTGCAAATATTCACAGAGCTCGTGG
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G45030.2 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------agcaacaatggaactatagaa------ctattatttaagatcttaagtttg------atataatttctaattaaagatgctgatctgaagtcatctcttaatttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
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gtgagatatctcttgcctatgatactttacttataatcgtttgcttgtgcttgaaagagtatattggaacttttagtaatgtaggtactacagcatggaacctattatagaaaactttactaatgccgcctatttatgttgccttctggaatcctttttttacttcatagtatcttgctttgatagGGTCCTGGAGGAGTTTGGTGTGATGTAGATGTTGTTGAGTTTCAATATTATGGTGCACCTGCGCAAACACCTAAAGAGCAGGTGTATACAGAGCTTGTTG
upper sequence: GLYMA20G02500.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g01870.t01 (Vitis vinifera), 3'ss of exon 3
---agcaacaatggaactatagaactattatttaagatcttaagtttgatataatttctaattaaagatgctgatctgaagtcatctcttaattt-ccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
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tactgcaact-tggtatggttcatatcttgacagggaaactaaacttgg-atattgttcaagttttcttgg-aagttgaaat-gcctttaaatctattgagcagGGACCAGGAGGCGTATGGTGTGATGTGGATGTTGTGGAATTCTCTTACTATGGTGCACCTGCACCAACACCCAAAGAACAATTGTATACTGAACTTGTCGMapped 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|14258572|gb|BG881480.1|BG881480EST: TTCACAGGCAATGGCTCAACCATATTCAGTGCCTACCTGCTGCCCTTGAG GGGCCGGGAGGTGTTTGGTGTGATGTGGATGTT
genomic: TTCACAGGCAATGGCTCAACCATATTCAGTGCCTACCTGCTGCCCTTGAGgtggggaatt ... ttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atataatttctaattaaagatgctgatctgaagtcatctcttaatttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
tttcc CT-rich tract
atttctaattaaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcaacaatggaactatagaactattatttaagatcttaagtttgatataatttctaattaaagatgctgatctgaagtcatctcttaatttccaaacagGGGCCGGGAGGTGTTTGGTGTGATGTGGATGTTGTGGAGTTCTCCTATTATGGTGCACCTGCACAAACTCCTAAAGAACAATTATATACGGAGCTTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - -caatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat