Sequence
atgc intronic sequence ATGC exonic sequence...agtgtaatttgccttttgttttatgttttagttttactgacaaaatgaagcttctatatgttttttaattattgtacttatcattttcataaaaaaatagGGCTGTTGACAAAGAAGTTCATCAATTTGATCAAACAAGCTGAGGATGGTATCCTTGATCTGAATAAAGCTGCTGACACATTAGAG
Basic information
species | Glycine max |
transcript | GLYMA12G09860.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 3
agtgtaatttgccttttgttttatgttttagttttactgacaaaatgaagcttctatatgttttttaattattgtacttatcattttcataaaaaaat--agGGCTGTTGACAAAGAAGTTCATCAATTTGATCAAACAAGCTGAGGATGGTATCCTTGATCTGAATAAAGCTGCTGACACATTAGAG
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-------------------gtaataactta-tttcattaactaa-tgtttaaaaaatgtacttttggataataagtttttttaatgatttaatctgcttcagGTCTTTTGACAAAGAAATTTATCAATTTGATAAAACAAGCAGAGGATGGTATTCTTGATCTAAACAAAGCAGCTGATACTTTAGAG
upper sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 3
agtgtaatttgccttttgtttt-atgttttagttttactgacaaaatga-agcttctatatgttttttaattattgtacttatcattt-tcataaaaaaatagGGCTGTTGACAAAGAAGTTCATCAATTTGATCAAACAAGCTGAGGATGGTATCCTTGATCTGAATAAAGCTGCTGACACATTAGAG
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---ttgttttattttttctatagatgttttcatttaatagtttgtgggacagccaaagtggatgccataaaagtgacaacaatgtcctatgattctcattcagGTCTCTTGACAAAGAAGTTCATTAATTTGATTAAACATGCAGAAGATGGTATTCTTGATCTAAATAAAGCTGCCGACACTTTAGAG
upper sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ05692 (Selaginella moellendorffii), 3'ss of exon 2
agtgtaatttgccttttgttttatgttttagttttactgacaaaatgaagcttctatatgttttttaattattgtacttatcattttcataaaaaaatagGGCTGTTGACAAAGAAGTTCATCAATTTGATCAAACAAGCTGAGGATGGTATCCTTGATCTGAATAAAGCTGCTGACACATTAGAG
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------------------------------gtatactttctcaagctgtgtttttggattctagctttttctagcgacctgtgttttcttcctgtg-cagGTCTTTTGACGAAGAAGTTTATTGACTTACTTAAGCAAGCTGAGGATGGTGTCCTTGATCTTAACAAAGCTGCAGAGACATTGAAA
upper sequence: GLYMA12G09860.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ05155 (Selaginella moellendorffii), 3'ss of exon 2
agtgtaatttgccttttgttttatgttttagttttactgacaaaatgaagcttctatatgttttttaattattgtacttatcattttcataaaaaaatagGGCTGTTGACAAAGAAGTTCATCAATTTGATCAAACAAGCTGAGGATGGTATCCTTGATCTGAATAAAGCTGCTGACACATTAGAG
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------------------------------gtatactttctcaagctgtgtttttggattctagctctttctagcggcctgtgttttcttcctgtg-cagGTCTTTTGACGAAGAAGTTTATTGACTTACTTAAGCAAGCTGAGGATGGTGTCCTTGATCTTAACAAAGCTGCAGAGACATTGAAAMapped 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|7588272|gb|AW704071.1|AW704071EST: AGGAAGTAATCTCACTCCTGCTGGTCCATGTCGTTATGACAGCTCTTTAG GGCTGTTGACAAAGAAGTTCATCAATTTGATCAAACAAGCTGAGGATGGTA
genomic: AGGAAGTAATCTCACTCCTGCTGGTCCATGTCGTTATGACAGCTCTTTAGgtattatagc ... aaaaaaatagGGCTGTTGACAAAGAAGTTCATCAATTTGATCAAACAAGCTGAGGATGGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaagcttctatatgttttttaattattgtacttatcattttcataaaaaaatagGGCTGTTGACAAAGAAGTTCATCAATTTGATCAAACAAGCTGAGGATGGTATCCTTGATCTGAATAAAGCTGCTGACACATTAGAG
ttttaat putative branch site (score: 3)
ttttttaattattgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgtaatttgccttttgttttatgttttagttttactgacaaaatgaagcttctatatgttttttaattattgtacttatcattttcataaaaaaatagGGCTGTTGACAAAGAAGTTCATCAATTTGATCAAACAAGCTGAGGATGGTATCCTTGATCTGAATAAAGCTGCTGACACATTAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - -ccttttg
- - - - - - - - - - - - - - - - - tactgac
- - - - - - - - - - - - - - - - - - - - -aaaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - -gcttcta