Sequence
atgc intronic sequence ATGC exonic sequencegtcagacgccagtttttcaggctgtttaattgtctgctgatatttcatgcctgagctagacagtccctttgaggtcttacagtctttttctcatactgcctttgttgggggatgaatttggtccatatttggcttgcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGGTTTCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACAAGCTGAAA
Basic information
species | Glycine max |
transcript | GLYMA01G41790.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 4
gtcagacgccagtttttcaggctgtttaattgtctgctgatatttcatgcctgagctagacagtccctttgaggtcttacagtctttttctcatactgcctttgttgggggatgaatttggtccatatttggcttgcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGGTTTCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACAAGCTGAAA
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-----------gtttgttcgact---taatagccttctcttgttt-gcatttga-----atagtttgcttgattttcaatgaggttttcttttccttaattttttttatttatcttttctttccccaccggtggtgcagTTTTACGTCGATACTGTGAAGAAAATGGCCCACTGCCATTTTCTATCTGGGTCACCTTTGCGAACATTGTGCCTTCTCATTGCTGGACAACCTGCAGATG
upper sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G47480.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcagacgccagtttttcaggctgtttaattgtctgctgatatttcatgcctgagctagacagtccctttgaggtcttacagtctttttctcatactgcctttgttgggggatgaatttggtccatatttggcttgcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGGTTTCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACAAGCTGAAA
| | || |||| || || | |||| | |||| || | ||||| | ||||||||||||||| || || ||||| |||||||| |||||||||||| | | ||||||||||| || ||||| ||||| || |||| || |||| |||||||
---------------------------------------------------------gttcctttcccttgattgctatagaactaaacgttccactgtagtgcttggttgactgacttggtgatgtcctaacttgcagTTCTATGTAGACACTGTGAAACAAATGGCCCTTCGCCAGCTGATACCCGGGTCACCTTTACGGACATTGTGCCTACTCGTTGCGGGACAACCAGCTGAAG
upper sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G47490.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcagacgccagtttttcaggctgtttaattgtctgctgatatttcatgcctgagctagacagtccctttgaggtcttacagtctttttc-tcatactgcctttgttgggggatgaatttggtccatatttggcttg---cagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGGTTTCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACAAGCTGAAA
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----------------------------------------------------------gtttgtttctcttgattgctatagaactaaacattgcactgtagtgcttggttgactgacttggtcgatgtcttaattgatgcagTTCTATGTTGACACTGTGAAACAAATGGCCCTTCGCCAGCTGGTACCCGGGTCACCTTTACGAACACTGTGCCTGCTGGTTGCAGGGCAACCAGCTGAAG
upper sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 4
gtcagacgccagtttttcaggctgtttaattgtctgctgatatttcatgcctgagctagacagtccctttgaggtcttacagtctttttctcatactgcctttgttgggggatgaatttggtccatatttggctt----gcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGGTTTCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACAAGCTGAAA
| | | | || | || | | ||||| || || || | | || ||| ||||| | |||||| ||||||||||| || |||||||||||| |||||||||| || |||| ||||||||||| ||| |||| || ||||||||||| |||| |||||
------------------------------------------------------gtttgtcctgattcttaaactcatttatcatttttttccaacaatgactggcagtaatttgcttgggtgtggttttggaatcaatgcagTTTTATGTTGATACTGTTAAGCAAATGGCAATTCGCCAGCTAGTACCAGGATCACCTTTGCGGACACTATGTCTGCTAATTGCTGGACAACCGGCTGATG
upper sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 5
-----------gtcagacgcca--gtttttcaggctgtttaattgtctgctgat-atttcatgcctgagctagacagtccctttgaggtcttacagtctttttctcatactgcctttgttgggggatgaatttggtccatatttggct--tgcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGGTTTCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACAAGCTGAAA
|| | | ||| || | || | | | || ||| ||||| |||| ||| || | ||| | || || ||| || | | | || || | ||||||| |||| |||||| ||||||||||||||||||| ||| | ||| |||| ||||||||||| || || ||||| ||||||| ||||| | ||| ||
gttctcatacaagcatatttaattgttctttccattcctttaccatatttgaattggctcaatcctgatctag-cagaggaattcattccttggatgtcaaacctgatttcaatttttatgctgacactctcttgtttcctttaatttcatgcagTTTTATGGTGATACCGTGAAGCAAATGGCACTTCAGCAGTTAGTTGCAGGATCACCTTTGCGGACGTTGTGCCTGTTAATTGCAGGGCAGCCAGCAGATGMapped 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|21888423|gb|BQ741636.1|BQ741636EST: GACAATTGTGGGGACCTGCACTTGTTCTGGCTTCACAACTTGGTGAACAG TTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGGTTTCAGGG
genomic: GACAATTGTGGGGACCTGCACTTGTTCTGGCTTCACAACTTGGTGAACAGgtcagacgcc ... tggcttgcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGGTTTCAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttctcatactgcctttgttgggggatgaatttggtccatatttggcttgcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGGTTTCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACAAGCTGAAA
atgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagacgccagtttttcaggctgtttaattgtctgctgatatttcatgcctgagctagacagtccctttgaggtcttacagtctttttctcatactgcctttgttgggggatgaatttggtccatatttggcttgcagTTCTATGTTGATACAGTGAAGCAAATGGCACTTCGCCAGCTGGTTTCAGGGTCACCTTTGCGCACATTATGCCTTCTAATTGCTGGGCAACAAGCTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA