Sequence
atgc intronic sequence ATGC exonic sequence...agaaaagagaaggaataaatataaaactaacaaactaacaacttttcgataaaaaagaaaatgcatcagttacattacatagccaaactttgtatggcagGTGGATTTAAGTGGAGGGTACTATGACGCAGGAGACAATGTGAAATTCAACTTTCCAATGGCCTACACCACTACCATGCTGTCATGGGCCACAATTGAAT
Basic information
species | Glycine max |
transcript | GLYMA04G12290.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G12290.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G71380.1 (Arabidopsis thaliana), 3'ss of exon 1
agaaaagagaaggaataaatataaaactaacaaactaacaacttttcgataaaaaagaaaatgcatcagttacattacatagccaaactttgtatggcagGTGGATTTAAGTGGAGGGTACTATGACGCAGGAGACAATGTGAAATTCAACTTTCCAATGGCCTACACCACTACCATGCTGTCATGGGCCACAATTGAAT
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------------------gtacacacct--taaaccat--atttaactttgatacagaatatatctttgtta-gtaacattgatata---tgaattgcagGTGGACTTAACCGGCGGGTACTATGACGCAGGAGACAACGTCAAGTTCAATTTACCAATGGCGTTTACCACCACAATGCTCTCATGGAGCGCACTGGAAT
upper sequence: GLYMA04G12290.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0089g00210.t01 (Vitis vinifera), 3'ss of exon 1
---agaaaagagaaggaataaatataaaactaacaaactaac-aacttttcgataaaaaagaaaatgcatcagttacattacatagccaaactttgtatggcagGTGGATTTAAGTGGAGGGTACTATGACGCAGGAGACAATGTGAAATTCAACTTTCCAATGGCCTACACCACTACCATGCTGTCATGGGCCACAATTGAAT
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tttaagtttaataacctcattttgctgcacttatacccaacttaaaccttggattttggttttaatac-tctatccaatctcat---caaacttttcatgacagGTTGATTTAACCGGTGGCTACTACGACGCGGGTGACAATGTGAAGTTCAACTTTCCCATGGCCTTCGCCACCACCATGCTGTCATGGGGCACCCTAGAAT
upper sequence: GLYMA04G12290.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------agaaaagagaaggaataaatata----aaactaacaaactaacaacttttcgataaaaaagaaaatgcatcagtt-acattacatagccaaactttgt-atgg------------cagGTGGATTTAAGTGGAGGGTACTATGACGCAGGAGACAATGTGAAATTCAACTTTCCAATGGCCTACACCACTACCATGCTGTCATGGGCCACAATTGAAT
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gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaaattgaccttgacgatggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGTMapped 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|4396432|gb|AI495429.1|AI495429EST: AGATCAAATTCTGGCCTCTTTGATGGTCGCCTAGCCAAT GTGGATTTAAGTGGAGGGTACTATGACGCAGGAGACAATGTGAAATTCAAC
genomic: AGATCAAATTCTGGCCTCTTTGATGGTCGCCTAGCCAATgtaacaatct ... tgtatggcagGTGGATTTAAGTGGAGGGTACTATGACGCAGGAGACAATGTGAAATTCAAC
EST:
gi|192306530|gb|FG996220.1|FG996220EST: AAATCAAATGGAGATCAAATTCTGGCCTCTTTGATGGTCGCCTAGCCAAT GTGGATTTAAGTGGAGGGTACTATGACGCAGGAGACAATGTGAAATTCAAC
genomic: AAATCAAATGGAGATCAAATTCTGGCCTCTTTGATGGTCGCCTAGCCAATgtaacaatct ... tgtatggcagGTGGATTTAAGTGGAGGGTACTATGACGCAGGAGACAATGTGAAATTCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgataaaaaagaaaatgcatcagttacattacatagccaaactttgtatggcagGTGGATTTAAGTGGAGGGTACTATGACGCAGGAGACAATGTGAAATTCAACTTTCCAATGGCCTACACCACTACCATGCTGTCATGGGCCACAATTGAAT
aaaaaagaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaaaagagaaggaataaatataaaactaacaaactaacaacttttcgataaaaaagaaaatgcatcagttacattacatagccaaactttgtatggcagGTGGATTTAAGTGGAGGGTACTATGACGCAGGAGACAATGTGAAATTCAACTTTCCAATGGCCTACACCACTACCATGCTGTCATGGGCCACAATTGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- aaaagaga
- - - - - -ggaataaa
- - - - - - - - - - - - -actaaca
- - - - - - - - - - - - - - - - - - - - - - - - -taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaact