Sequence
atgc intronic sequence ATGC exonic sequence...aaatgaacatagtaagctactacagaagaatttaacaattgactttttcaaaattaatattaaatgatttctcacaatttattcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGTTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAGTC
Basic information
species | Glycine max |
transcript | GLYMA06G06890.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G06890.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 4
aaatgaacatagtaagctactacagaagaatttaacaattgactttttcaaaattaatattaaatgatttctcacaatttattcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGTTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAGTC
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-----------gtatgtcagctcacagatacc-attatcaggccttcctgcatttccttttctaccactgat----gctcatgtttcttaacctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATC
upper sequence: GLYMA06G06890.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g19650.1 (Oryza sativa), 3'ss of exon 4
aaatgaacatagtaagctactacagaagaatttaa--caattgactttttcaaaattaatattaaatgatttctcacaatttattcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGTTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAGTC
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--atgccgtttggccacttgtgccctctcttttcatccattttgggtgttcatcacaggatgtacataactgaattcctctcccttttttttcgtcatgtagGAGGAAGACAAGGCACGGCTAGTCCAAGAAACAGGGCTACAGCTAAAGCAGATCAACAACTGGTTCATCAACCAAAGGAAAAGAAACTGGCACAGTAACC
upper sequence: GLYMA06G06890.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
aaatgaacatagtaagctactacagaag--aatttaacaattgactttttcaaaattaatattaaatgatttctcacaatttattcttcaat-gttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGTTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAGTC
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------gtatgtgacactacggcgacatataattccctcgtcaacttttgcta--tcagcttgggttcattgct---gatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
upper sequence: GLYMA06G06890.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
aaatgaacatagtaagctactacagaagaatttaacaattgactttttcaaaattaatattaaatgatttctca-caatttattcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGTTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAGTC
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----gtacgtgaca--ccgcgtcaacttaattccctcgttagcttctgcta--tcaggttcggctcattgatgagcaactctttgctta---ctcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACCMapped 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|298195893|gb|HO044284.1|HO044284EST: CTGTCCTTAAAGCTTGGTGGCAATCACATTCCAAGTGGCCTTATCCTACG GAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGTTAAAGCAG
genomic: CTGTCCTTAAAGCTTGGTGGCAATCACATTCCAAGTGGCCTTATCCTACGgtaagaactc ... gttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGTTAAAGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcaaaattaatattaaatgatttctcacaatttattcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGTTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAGTC
ttctcac putative branch site (score: 2)
tgttttttc putative PPT
aaattaatattaaatg 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
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aaatgaacatagtaagctactacagaagaatttaacaattgactttttcaaaattaatattaaatgatttctcacaatttattcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGTTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA