Sequence
atgc intronic sequence ATGC exonic sequencegtaaggagtgcttgtatttctggttttggcaaacctaaagcatgttattgtcttgcttagatgaaaagattagaagtgtgtctgttagtcaagatgtaacgatttccttatttatgcagtgatgctactagatttttgtttaatttgggtagaattccttttatatagGAGGCTAAAAACACTGCAGCTCTGAAGGCTCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTTCAGAGAATGGTTATTGGTAATCAG
Basic information
species | Glycine max |
transcript | GLYMA13G00980.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 4
gtaaggagtgcttgtatttctggttttggcaaacctaaagcatgttattgtcttgcttagatgaaaagattagaagtgtgtctgttagtcaagatgtaacgatttccttatttatgcagtgatgctactagatttttgtttaatttgggtagaattccttttatatagGAGGCTAAAAACACTGCAGCTCTGAAGGCTCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTTCAGAGAATGGTTATTGGTAATCAG
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-------------------------------------------------------------------------------gttcgttcttc------tatcaattcttgtttgtattctttgccaatcttgaacttctatttatttc--------ttctgaccac-cagGAGGCCAAAAACACTGCAACTTTGAAGGCTCAGATTGACAAGCTGCAACAGGAACGCGATGAGTTCCAAAAAATGGTTATTGGCAATCAG
upper sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 5
gtaaggagtgcttgtatttctggttttggcaaacctaaagcatgttattgtcttgcttagatgaaaagattagaagtgtgtctgttagtcaagatgtaacgatttccttatttatgcagtgatgctactagatttttgtttaatttgggtagaattccttttatatagGAGGCTAAAAACACTGCAGCTCTGAAGGCTCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTTCAGAGAATGGTTATTGGTAATCAG
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-----------------------------------------------------------------------------------gtttgtcct--tgtatcaactctttggtttcttcaccattttt--tggattctaaattcttttc-----aattacc-------agGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG
upper sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaaggagtgcttgtatttctggttttggcaaacctaaagcatgttattgtcttgcttagatgaaaagattagaagtgtgtctgttagtcaagatgtaacgatttccttatttatgcagtgatgctactagatttttgtttaatttgggtagaattccttttat--atagGAGGCTAAAAACACTGCAGCTCTGAAGGCTCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTTCAGAGAATGGTTATTGGTAATCAG
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-----------------------------------------------------------------------------------gtgagtcc---tataaagtttcagctgaaattgtttt--cgct--taggctcttgtttgatt----atgaattcactgtgttgacagGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG
upper sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 5
gtaaggagtgcttgtatttctggttttggcaaacctaaagcatgttattgtcttgcttagatgaaaagatta-gaagtgtgtctgttagtcaagatgtaacgatttccttatttatgcagtgatgctactagatttttgtttaatttgggtag-aattccttttatatagGAGGCTAAAAACACTGCAGCTCTGAAGGCTCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTTCAGAGAATGGTTATTGGTAATCAG
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---------------------------------------------------gttaggaacacttaaattttgtaaagtgaaataatctaggaaattggaattaccctattagacattctatgtcagttgtgtctgtttgtt-gatcggtgtagtagttgtgtatgattagGAAGCAAAAGCTACAGCAGCTTTTAAGGCTCAAATAGAAAAATTGCAGCAGGAGCGGGATGAATTTCAAAGGATGGTTATTGGTAATCAGMapped 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|7284560|gb|AW597148.1|AW597148EST: AAGGTCTACTACAAGTCAAGGACAGGGAGATAGCGACTATTACTAGAACG GAGGCTAAAAACACTGCAGCTCTGAAGGCTCAGATTGAGAAGCTGCAACAG
genomic: AAGGTCTACTACAAGTCAAGGACAGGGAGATAGCGACTATTACTAGAACGgtaaggagtg ... ttttatatagGAGGCTAAAAACACTGCAGCTCTGAAGGCTCAAATTGAGAAGCTGCAACAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcagtgatgctactagatttttgtttaatttgggtagaattccttttatatagGAGGCTAAAAACACTGCAGCTCTGAAGGCTCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTTCAGAGAATGGTTATTGGTAATCAG
gtttaat putative branch site (score: 4)
ttccttttat putative PPT
tactagatttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggagtgcttgtatttctggttttggcaaacctaaagcatgttattgtcttgcttagatgaaaagattagaagtgtgtctgttagtcaagatgtaacgatttccttatttatgcagtgatgctactagatttttgtttaatttgggtagaattccttttatatagGAGGCTAAAAACACTGCAGCTCTGAAGGCTCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTTCAGAGAATGGTTATTGGTAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG