Sequence
atgc intronic sequence ATGC exonic sequence...aattgacaacccattattccttttccttttatgctacaagtattcaaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA
Basic information
species | Glycine max |
transcript | GLYMA01G40650.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G40650.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g01014.1 (Oryza sativa), 3'ss of exon 5
aattgacaacccattattccttttccttttatgctacaagtattc-aaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA
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--gtatgaattc--tactgctttcagttcgatggaaatggagtcctgaatttgggatatttgcgctgat--cttaactgtg--ctgattgatatg-tgtagAGTGGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGA
upper sequence: GLYMA01G40650.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G17840.1 (Arabidopsis thaliana), 3'ss of exon 5
-aattgacaacccattattccttttccttttatgctacaagtattcaaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA
||| | | ||| |||||| | | || | || | || | ||| | | || | |||| | ||| || || || | |||| || | |||| |||||||| ||||||||||||| |||||| || | ||||||| | || |||||||||||||| ||||| ||||| || ||||
gtattatagattttctgttc---ttccttgtctccttcttgttccttgaactcg---tttaagt---gtatttgacttttaatt-gtttg--aattttcagACTGGACTCTTGCCACCATTTGTACCATTTGCTCAAGTATTTGCAGCCACTATTACAGCCGCTCTCACTGGTTCTCTCTACTACATAGCTGCTTCCCCTA
upper sequence: GLYMA01G40650.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0012g01220.t01 (Vitis vinifera), 3'ss of exon 5
aattgacaacccattattccttttccttttatgctacaagtattcaaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA
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------------gtaagagctccttcctt--ggtttcggactgtcatgacaactgaatttat------atcttact-gtgaattctt---caaattgtagACTGGAGTGCTGCCTCCATTTGTGCCATTTGCCCAGGCGTTTGCAGCTGTAATCACAGCTGCTCTTACTGGTTCCCTCTATTATGTGGCTGCCTCTCCAAMapped 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|11274513|gb|BF324866.1|BF324866EST: TTTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATTG ACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTT
genomic: TTTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATTGgtatgtatgt ... taaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTT
EST:
gi|17022600|gb|BM093634.1|BM093634EST: TTTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATTG ACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTT
genomic: TTTTACGAGGCAGTAATCTTATAACAGATGTTCAAGGAATGGCATCATTGgtatgtatgt ... taaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA
gactaac putative branch site (score: 1)
taaaatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattgacaacccattattccttttccttttatgctacaagtattcaaagctagaagtttcattctggtgactaacttgtgatttgtatggtaaaatgtagACCGGTGTGCTGCCTCCATTTGTTCCATTTGCTCAAGCATTTGCGGCTGTTCTTACAGCTGTCCTTACTGGTTCTCTCTATTACATGGCTGCCTCTCCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG