Sequence
atgc intronic sequence ATGC exonic sequencegtaatttaaataattactcaagatttatttataacactaaatgcatgcatcttgactctttattatagtattgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT
Basic information
species | Glycine max |
transcript | GLYMA04G39110.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39110.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g10100.2 (Oryza sativa), 3'ss of exon 5
gtaatttaaataattactcaagatttatttataacactaaatgcatgcatcttgactctttattatagtat-tgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT
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----gtatgatacttgatataatggtattt-tgtttttgtggaaccacatgttg-ctcttagttctaatctatgaaacatcacttttctcacagGGATATCAAAGGGGCCAACATACTTGTAGATCCTAATGGTGACATCAAACTTGCTGATTTTGGGATGGCCAAGCAT
upper sequence: GLYMA04G39110.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g35700.1 (Oryza sativa), 3'ss of exon 5
gtaatttaaataattactcaagatttatttataacactaaatgcatgcatcttgactctttattatagtattgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT
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gtagtacagat---tatccacagttgttttacattcctttggtagtaaaagaaataccttaaccacttcatcc-----tgtttctcttcgcagAGATATTAAAGGTGCTAACATACTTGTCGGCCCTAATGGTGAAGTCAAACTTGCTGACTTTGGCATGGCTAAGCAT
upper sequence: GLYMA04G39110.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g35010.1 (Oryza sativa), 3'ss of exon 5
gtaatttaaataattactcaagatttatttataacactaaatgcatgcatcttgactctttattatagtattgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT
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gtaatgtaaattatcctaca----ctgttagtgattttcatggtaggcactgaatacaatgatcactttgtaaattttatttt-tgtggacagAGACATTAAAGGAGCAAACATACTTGTGGGCCCTAATGGTGAAGTCAAACTTGCGGACTTTGGCATGGCTAAACAT
upper sequence: GLYMA04G39110.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G140726_T01 (Zea mays), 3'ss of exon 5
gtaatttaaataattactcaagatttatttataacactaaatgcatg--catcttg-actctttattatagtattgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT
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----gttgttttgttgtctaaaactgtcttctcattccataggtatagtcatatagcacagaatgcaataatcatgtcatactttt-ttttggcagAGATATCAAAGGAGCAAACATACTCGTGGGTCCTAATGGTGAAGTCAAGCTGGCTGACTTTGGCATGGCTAAGCAT
upper sequence: GLYMA04G39110.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G064773_T01 (Zea mays), 3'ss of exon 1
gtaatttaaataattactcaagatttatttataacactaaatgcatgcatcttgactctttattatagtattgata----agtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT
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----gttgttttgttgtctaaaactgtgttctcattccatacgtatagtcatatagcacagaatggaataatcatatcatacttattttcttggcagATATATCAAAGGAGCAAACATACTTGTGGGTCCTAATGGTGAAGTAAAGCTTGCTGACTTTGGCATGGCTAAGCAT
upper sequence: GLYMA04G39110.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G53570.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaatttaaataattactcaagatttatttataacactaaatgcatgcatcttgactctttattatagtattgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT
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gtattcaaaatgacatcttaaaggttgaatggaattcaatttgtct-cttcttggacatttaataaagagtta------ttttgttctaacagGGACATCAAAGGAGCAAATATATTAGTGGATCCGAATGGTGAAATCAAGTTGGCAGACTTTGGGATGGCCAAACAT
upper sequence: GLYMA04G39110.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0044g01290.t01 (Vitis vinifera), 3'ss of exon 5
gtaatttaaataattactcaagatttatttataacactaaatgcatgcatcttgactctttattatagtattgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT
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gta--ctgggttgtggtt--atgattacttgtatgagattgctgattcctcttatttctggcaactcagataaatatattttt-tcatggcagGGATATCAAAGGGGCAAACATATTAGTGGGACCTAATGGGGAGATCAAGTTGGCTGATTTTGGCATGGCAAAACATMapped 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|10845792|gb|BF068837.1|BF068837EST: CAGATTGTCTCTGGACTTTCCTATCTTCATGGGAGAAATACAGTACATAG GGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCT
genomic: CAGATTGTCTCTGGACTTTCCTATCTTCATGGGAGAAATACAGTACATAGgtaatttaaa ... attttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgcatgcatcttgactctttattatagtattgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT
tttttattttc CT-rich tract
actctttattatagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttaaataattactcaagatttatttataacactaaatgcatgcatcttgactctttattatagtattgataagtttttattttcacagGGATATCAAAGGGGCTAACATACTAGTTGATCCTAATGGTGAAATCAAGCTGGCAGACTTTGGAATGGCTAAACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG