Sequence
atgc intronic sequence ATGC exonic sequencegtaaggagatgcttggaaatctggttttggcaaacgtaaagcatgctattgtcttgcttagatgaaaagatcagaagtgtgtccattatgcaagatgcaacaatttccttttttacgcagtgatgctgctagattttgtttaactggggttgaattcctgttatttagGAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTCCAGAGAATGGTTATTGGTAATCAG
Basic information
species | Glycine max |
transcript | GLYMA17G07040.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 4
gtaaggagatgcttggaaatctggttttggcaaacgtaaagcatgctattgtcttgcttagatgaaaagatcagaagtgtgtccattatgcaagatgcaacaatttccttttttacgcagtgatgctgctagattttgtttaactggggttgaattcctgttatttagGAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTCCAGAGAATGGTTATTGGTAATCAG
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--------------------------------------------------------------------------------gttcgttcttc------tatcaattcttgtttgtattctttgccaatcttgaacttctatttattt--------cttctgaccaccagGAGGCCAAAAACACTGCAACTTTGAAGGCTCAGATTGACAAGCTGCAACAGGAACGCGATGAGTTCCAAAAAATGGTTATTGGCAATCAG
upper sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 5
gtaaggagatgcttggaaatctggttttggcaaacgtaaagcatgctattgtcttgcttagatgaaaagatcagaagtgtgtccattatgcaagatgcaacaatttccttttttacgcagtgatgctgctagattttgtttaactggggttgaattcctgttatttagGAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTCCAGAGAATGGTTATTGGTAATCAG
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--------------------------------------------------------------------------------------------------gtttgtccttgtatcaactctttggtttcttcaccattttttggattctaaattcttttcaattacc-agGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG
upper sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaaggagatgcttggaaatctggttttggcaaacgtaaagcatgctattgtcttgcttagatgaaaagatcagaagtgtgtccattatgcaagatgcaacaatttccttttttacgcagtgatgctgctagattttgtttaactggggttgaattcctgttatt--tagGAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTCCAGAGAATGGTTATTGGTAATCAG
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-----------------------------------------------------------------------------------------gtgagtcctataaagtttcagctgaaattgttttcgct-taggctcttgtttgatta----tgaattcactgtgttgacagGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG
upper sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 5
gtaaggagatgcttggaaatctggttttggcaaacgtaaagcatgctattgtcttgcttagatgaaaagatcagaagtgtgtccattatgcaagatgcaacaatttccttttttacgcagtgatgctgctagattttgtttaactggggttgaattcctgt-tatttagGAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTCCAGAGAATGGTTATTGGTAATCAG
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-----------------------------------gttaggaacacttaaattttg-taaagtgaaataatctaggaaattggaattaccc----tattagacattctatgt-----cagttgtgtc------tgtttgttgatcggtgtagtagttgtgtatgattagGAAGCAAAAGCTACAGCAGCTTTTAAGGCTCAAATAGAAAAATTGCAGCAGGAGCGGGATGAATTTCAAAGGATGGTTATTGGTAATCAGMapped 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|192323206|gb|FK016337.1|FK016337EST: AAGGTCAACTACAAGTCAAAGACAGGGAGATAGCGACTATTACTAGAACG GAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAG
genomic: AAGGTCAACTACAAGTCAAAGACAGGGAGATAGCGACTATTACTAGAACGgtaaggagat ... tgttatttagGAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacgcagtgatgctgctagattttgtttaactggggttgaattcctgttatttagGAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTCCAGAGAATGGTTATTGGTAATCAG
gtttaac putative branch site (score: 3)
ttcctgtt putative PPT
tagattttgtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggagatgcttggaaatctggttttggcaaacgtaaagcatgctattgtcttgcttagatgaaaagatcagaagtgtgtccattatgcaagatgcaacaatttccttttttacgcagtgatgctgctagattttgtttaactggggttgaattcctgttatttagGAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTCCAGAGAATGGTTATTGGTAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG