Sequence
atgc intronic sequence ATGC exonic sequence...tggtggctaatttgtttagagttctgatggatattgtgtagtatcttttgtggtaataataatgcatgcaatacccagattaaaaatcctacatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
Basic information
species | Glycine max |
transcript | GLYMA02G36530.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g24650.1 (Oryza sativa), 3'ss of exon 5
tggtggctaatttgtttagagttctgatggatat-tgtgtagtatcttttgtggtaataataatgcatgcaatacccagattaaaaatcctacatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
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------gtacttccctt----ttcagttacttgtgtgagcaagcactggtttacttgttatggtgtatctacta--------ataatttccctgatcacagGTTCATTTTATTTCTGCTGCATGCGAAAATATGATAAGTGGCACAGGCATGAGGCCTGGTGACATTGTGACTGCTTCTAATGGAAAAACTATTGAG
upper sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 5
tggtggctaatttgtttagagttctgatggatattgtgtagtatcttttgtggtaataataatgcatgcaatacccagattaaaaatcc--tacatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
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---------gtaagttta----tcacacggagcttgcgt------ttctgagttaa-----atgaatg---tacctaaacaaatgcttcgttgcacaatcagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG
upper sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 6
tggtggctaatttgtttagagttctgatggatattgtgtagtatcttttgtggtaataataatgcatgcaatacccagattaaaa--atcctacatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
| | | | | | || || | ||| | | | | || | | || | || ||||||||||| || |||||||| ||||| |||||||| |||||||| || ||||| ||||||||| | |||| || ||||| |||||||| || |||
-------------------------gttagtttctcccatcagattcttttgaaagctatagtttgttaaccgaactgaacagattcgtcttccacaaccagGTTCATTTCATCGTTGCAGCCTGTGAAAATATGATTAGTGGAACCGGAATGAGACCTGGAGATGTCATCACTGCCTCAAACGGAAAGACCATTGAG
upper sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G30910.1 (Arabidopsis thaliana), 3'ss of exon 5
tggtggctaatttgtttagagttctgatggatattgtgtagtatcttttgtggtaataataatgcatgcaatacccagattaaaaatcct--acatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
| ||||| || | ||| ||| || || || | ||| || ||| |||| | || | || || |||| || ||||| || |||||||||||||||||||||||||| || || ||||| ||||||||| | ||||||| ||||| || ||||| || |||
---------gtaagttta----tcacacggagcttgagt------ttctgagttaa-----gtgaatg---tacctgaacaaatgcttctttgcacaattagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACCGGAATGAGACCTGGAGATGTCATCACAGCCTCAAACGGGAAGACAATTGAG
upper sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0037g00180.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------tggtggctaatttgtttag-agttctgatggatattgtgtagtatcttttgtggtaat--aataatgcatgcaatacccag--attaaaaatcctacatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
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gtaagccagttgttgttgttgttgttatcattgtttgtttgttttaacttgcatggaacaatttcttaactaatccatttgtatgttctattttcaattctccagcaattgaatctagcatacacttatgacttattaagggtcttgtatttgcagGTGCATTTCATTGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGCATGAGGCCTGGAGACGTTGTCACAGCTTCAAATGGAAAGACAATTGAGMapped 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|151406149|gb|EV275964.1|EV275964EST: TTTTAGGAACAGCAAAAGCTCTCGGTCAAATCAAACCTCTTGGGGTGGAG GTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATG
genomic: TTTTAGGAACAGCAAAAGCTCTCGGTCAAATCAAACCTCTTGGGGTGGAGgtcagtcatt ... acatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATG
EST:
gi|192304831|gb|FG997041.1|FG997041EST: TTTTAGGAACAGCAAAAGCTCTCGGTCAAATCAAACCTCTTGGGGTGGAG GTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATG
genomic: TTTTAGGAACAGCAAAAGCTCTCGGTCAAATCAAACCTCTTGGGGTGGAGgtcagtcatt ... acatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgtggtaataataatgcatgcaatacccagattaaaaatcctacatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
taataataatgcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggtggctaatttgtttagagttctgatggatattgtgtagtatcttttgtggtaataataatgcatgcaatacccagattaaaaatcctacatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- gtggcta
- - - - - - - - - - - tctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acccaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaatcc