Sequence
atgc intronic sequence ATGC exonic sequence...gttaattgtctgaggcatcccacttgtttctcttgtgctgatcatatctttttcataggtctaataccgttcttctccttcccttttttttttctgtaagATTCAAAGAAATCTACAGTTGCGAATAGAAGAACAAGGAAGGTACCTCCAGATGATGTTTGAGAAGCAATGTAAACCTGGAAATGAAACGTTCAAGGCAC
Basic information
species | Glycine max |
transcript | GLYMA13G18800.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G18800.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G006477_T01 (Zea mays), 3'ss of exon 7
--gttaattg--tctgaggcatcccacttgtttctcttgt-gctgatcatatctttttcataggtctaataccgttcttctccttcccttttttttttctgtaagATTCAAAGAAATCTACAGTTGCGAATAGAAGAACAAGGAAGGTACCTCCAGATGATGTTTGAGAAGCAATGTAAACCTGGAAATGAAACGTTCAAGGCAC
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aaacgaacgggccctaagtgattttgcccaacattaatattaatgccaatgaagcttgctttatcctaacactatatatatatatattcctatattgc-----agATTCAGCGAAAATTGCAGTTGCGGATTGAAGAGCAAGGAAAGTATCTGCAGATGATGTTTGAAAAGCAGAGTCAATCGAGCACGGAGAAAGTCCAGGATC
upper sequence: GLYMA13G18800.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G28610.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------gttaattgt-ctgaggcatcccacttgtttctcttgtgctgatcatat----ctttttcatagg----tctaataccgttctt--ctccttcccttttttttttctgtaagATTCAAAGAAATCTACAGTTGCGAATAGAAGAACAAGGAAGGTACCTCCAGATGATGTTTGAGAAGCAA---TGTAAACCTGGAAATGAAACGTTCAAGGCAC
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gtatgttcataaaggcattgccattagctttggttttttatacttatgtgtttggattgtagctgctaaagagaaaatgtgaaacctgtttataaagtattctgaatttgggtatgacatgtgttcttttcctttgcctgcagATTCAAAGAAACCTGCAACTCCGAATAGAAGAACAAGGCAAGTACCTGCAAATGATGTTCGAGAAGCAAAACTCTGGTCTTACCAAAGGGACAGCCTCAA---
upper sequence: GLYMA13G18800.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g04120.t01 (Vitis vinifera), 3'ss of exon 7
gttaattgtctgaggcatcc---cacttgtttctcttgtgctgatcatatcttt-ttcataggtctaataccgttcttctccttcccttttttttttctgtaagATTCAAAGAAATCTACAGTTGCGAATAGAAGAACAAGGAAGGTACCTCCAGATGATGTTTGAGAAGCAATGTAAACCTGGAAATGAAACGTTCAAGGCAC
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---tacacaaagagacatgcatatatatataagcataaagagaattgcatattagttcatatccatgatttttatgtaatattggtaactttcatggtcgca-gATACAAAGAAATTTACAGCTGCGAATAGAAGAACAAGGGAGATACCTCCAAATGATGTTTGAGAAGCAATGCAAATCAGGAATTGACAAGCTGAAGACATMapped 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|24136533|gb|BU927043.1|BU927043EST: CTCTACGACTACAAATGGAGGTTCAGAAGCGGTTGCATGAACAGCTTGAG ATTCAAAGAAATCTACAGTTGCGAATAGAAGAACAAGGAAGGTACCTCCAG
genomic: CTCTACGACTACAAATGGAGGTTCAGAAGCGGTTGCATGAACAGCTTGAGgtttgaactt ... tttctgtaagATTCAAAGAAATCTACAGTTGCGAATAGAAGAACAAGGAAGGTACCTCCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctttttcataggtctaataccgttcttctccttcccttttttttttctgtaagATTCAAAGAAATCTACAGTTGCGAATAGAAGAACAAGGAAGGTACCTCCAGATGATGTTTGAGAAGCAATGTAAACCTGGAAATGAAACGTTCAAGGCAC
gtctaat putative branch site (score: 3)
tctaataccgttcttc CT-rich tract
ttttttttttctgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaattgtctgaggcatcccacttgtttctcttgtgctgatcatatctttttcataggtctaataccgttcttctccttcccttttttttttctgtaagATTCAAAGAAATCTACAGTTGCGAATAGAAGAACAAGGAAGGTACCTCCAGATGATGTTTGAGAAGCAATGTAAACCTGGAAATGAAACGTTCAAGGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - -ctgaggc
- - - - - - - - -tcccact
- - - - - - - - - - - - - - - - - -tgctgat