Sequence
atgc intronic sequence ATGC exonic sequence...cttcagatgttagctggaaaaaagaaaagaaaacattgagcgattatgtttcttgattaatgacattttgatttttaaaattttgttaattattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG
Basic information
species | Glycine max |
transcript | GLYMA10G11720.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G11720.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G033592_T01 (Zea mays), 3'ss of exon 13
------cttcagatgttagctggaaaaaagaaaagaaaacattgagcgattatgtttcttgattaatgacattttgatttttaaaattttgttaattattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG
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ttcatctttcatgatatacatgtgtttcagaactgatgtatttt--cagtgctgtatctaatccgactacttatgcagtgtttgactcttgctc----ttctctagATTGGCGTTGGCATGTGCATGGAGGGAATAGAGCACAATCCAGTTGTTTATGAACTTATGTCTGAAATGGCATTTCATAATAAGAAGGTTGAGGTTGAG
upper sequence: GLYMA10G11720.2 (Glycine max), 3'ss of exon 13
lower sequence: AT5G13690.1 (Arabidopsis thaliana), 3'ss of exon 13
cttcagatgttagctggaaaaaagaaaagaaa----acattgagcga-ttatgtttcttgatta-atgacattttgatttt-----taaaattttgttaattattttgca----gGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG
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--gtaactcataactacgacattcacaatatgtttcacattttttatcttatgtctataggtgagactattttctccgcttagaaatggaatcttgttatttatgttgcacatagGTCGGTGTAGGAATGTGCATGGAAGGAATAGAGCAGAACCCGGTGGTTTACGAACTAACTTCTGAAATGGCATTTCGAGATGAGAAAGTTGATGTACAG
upper sequence: GLYMA10G11720.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv13s0064g00370.t01 (Vitis vinifera), 3'ss of exon 13
cttcagatgttagctggaaaaaagaaaagaaaacatt-gagcgattatgtttcttgattaatgacattttgatttttaaaattttgttaat-tattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG
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actaaacttttggatgtttatattccagtatatcatttgacctcctatgtt-cttgag-gaggttattgacatggctcactaattattgatgtttcccatagGTTGGTGTTGGCATGTGCATGGAAGGAATTGAGCAAAACCCAGTTGCTTATGAGCTGATGTCTGAAATGGCATTTCGCAGTGAAAAAGTTCAACTTGTG
upper sequence: GLYMA10G11720.2 (Glycine max), 3'ss of exon 13
lower sequence: PP1S329_23V6.1 (Physcomitrella patens), 3'ss of exon 13
---------cttcagatgttagctggaaaaaagaaaagaaaacattgagcgattatgtttcttgattaatgacattttgatttttaaaattttgttaattattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG
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gtaggattggtgaaagttttggttggttgtaatacagcaaagaat---gttatcggggcgtgt-attaatcgtctctt---tcttcactgtgtgttga--gtctggcagGTAGGTGTTGGCATGTGTATGGAAGGCATTGAGCAGAACCCAGTTGTGTATGACTTGATGGCTGAAATGGCATTTCACAATGCAACCGTCGTTGTCGAGMapped 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|192322077|gb|FK012181.1|FK012181EST: CAATTTCTTCAGGGCCTGTTGATGCTCGTGTCAGTGCAAACTCAACAATG GTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTAT
genomic: CAATTTCTTCAGGGCCTGTTGATGCTCGTGTCAGTGCAAACTCAACAATGgtactttcaa ... tattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtttcttgattaatgacattttgatttttaaaattttgttaattattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG
tgttaat putative branch site (score: 3)
ttatttt CT-rich tract
attaatgacattttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcagatgttagctggaaaaaagaaaagaaaacattgagcgattatgtttcttgattaatgacattttgatttttaaaattttgttaattattttgcagGTAGGTGTTGGTATGTGCATGGAAGGAATAGAACAGAACCCTATTGTTTATGAGTTGATGTCTGAAATGGCATTTCGTGATAAGAAAGTTAAAGTTTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - -aaaagaa
- - - - - - - - - - -aagaaaa