Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgaatcttccttttttgttggagccactactggcatattgcaggagattggaatcaacgagaatgattttgaaccatagtattaacaaagctgcaattgataaatgtggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACGATCTCA
Basic information
species | Glycine max |
transcript | GLYMA10G33680.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 5
gtttgtgaatcttccttttttgttgg--agccactactggcatattgcaggagattggaatcaacgagaatgattttgaaccatagtattaacaaagctgcaattgataaatgtggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACGATCTCA
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----gtaactgctgatctgcaatgagttagaaagctgtgtcatgtttt------ttcctctcttctcagttctctctaagacactccatgcttta---tatattcattattctcttttatagGTTGGTACTATATCAGCTAATGGGGAAAGGGAAATTGGTGAGCTCATTGCAAAAGCTATGGAGAAGGTTGGCAAAGAGGGAGTCATCACTATTACG
upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 5
gtttgtgaatcttccttttttgttggagccactactggcatattgcaggagattggaatcaacgagaatgattttgaaccatagtat-taacaaagctgcaattgataaatgtggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACGATCTCA
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-------------------------gtaatacttgtgattcattgcagatctcattatgtgtttgacttgtttcttaatcttaatctgttactaagttcttatgttcatatataa----agGTGGGCACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCG
upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
gtttgtgaatcttccttttttgttggagccactactggcatattgcaggagat-tggaatcaacgagaatgattttgaaccatagtattaacaaagctgcaattgataaatgtggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACGATCTCA
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-----------------------------------------------gtatatctgcaaggctctagttttatgttc--ccttcatctttttaaaattc---tttctctatcctgtga-agGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 4
gtttgtgaatcttccttttttgttggagccactactggcatattgcaggagattggaatcaacgagaatgattttgaaccatagtattaacaaagctgcaattgataaatgtggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACGATCTCA
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----------------------------gtatatctgcagcaccctagttactttattttgttcttatcctgtccatccctcacctttttttattctctctatcctgtatgtaaagGTGGGT----ACAATATCAGCAAATGGAGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCG
upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 5
---------------------------------gtttgtgaatcttccttttttgttggagccactac-tggcatattgcaggagattggaatcaacgagaatgattttgaaccatagtattaacaaagc--tgcaattgataaatgtggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACGATCTCA
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gtaagcaaatcaccatctgaaggtgatactagaattttagcatcttgtttttgggcttaaactctaatatagaaaatctcgtggatgtgttgccgaagctactaatggaagtcacttcaacggatcattccttgcttttgtgtggtgttctgccagGTTGGAACAATCTCTGCGAATGGAGACCGAGAAATTGGTGACTTGCTAGCTCGTGCTATGGAGAAGGTTGGCAAGGAGGGTGTCATCACTGTCTCTMapped 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|208170087|gb|GD966522.1|GD966522EST: ATCTGAAAAGCAGAGCACGGATGATTAGCACTTCTGAAGAAATTGCCCAG GTTGGAACAATATCTGCCAA
genomic: ATCTGAAAAGCAGAGCACGGATGATTAGCACTTCTGAAGAAATTGCCCAGgtttgtgaat ... gtggtgatagGTTGGAACAATATCTGCCAA
EST:
gi|192326928|gb|FK015155.1|FK015155EST: ATCTGAAAAGCAGAGCACGGATGATTAGCACTTCTGAAGAAATTGCCCAG GTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCA
genomic: ATCTGAAAAGCAGAGCACGGATGATTAGCACTTCTGAAGAAATTGCCCAGgtttgtgaat ... gtggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatgattttgaaccatagtattaacaaagctgcaattgataaatgtggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACGATCTCA
atagtattaacaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgaatcttccttttttgttggagccactactggcatattgcaggagattggaatcaacgagaatgattttgaaccatagtattaacaaagctgcaattgataaatgtggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACGATCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG