Sequence
atgc intronic sequence ATGC exonic sequencegttattttgttttattgatctgctccccctttttactgactgttttatatttttattgtattaaaagttgaaattaatatgatcactaatcaagctttctaattgttgattgtctagtgtcttctcaattcttattattatgaatatcctgataccagtttaatcttttaatgtagACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAAATTCGTAGTAAAAGAATTAAGAAAGCGGTAAAAGGAATCACTGGTAAGC
Basic information
species | Glycine max |
transcript | GLYMA01G16370.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os03g10780.1 (Oryza sativa), 3'ss of exon 12
gttattttgttttattgatctgctccccctttttactgactgttttatatttttattgtattaaaagttgaaattaatatgatcactaatcaagctttctaattgttgattgtctagtgtcttctcaattcttattattatgaatatcctgataccagtttaatcttttaatgtagACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAAATTCGTAGTAAAAGAATTAAGAAAGCGGTAAAAGGAATCACTGGTAAGC
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-------------------------------------------------------------------------ttcatttaactaagagtgatttaaccggaatgtcagcaatccaaagtctgcaaaattgg-gttatt-taaattttacagtttca-tgtgtcacacacatgcagACTCAACTACGCATGGAGGCGTTTTACTCATTCAATGAGAGATTTGCAAAAATTCGTAGCAAAAGGATTAAGAAAGCTATCAAGGGTATTACAGGGAAAA
upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G388915_T01 (Zea mays), 3'ss of exon 13
gttattttgttttattgatctgctccccctttttactgactgttttatatttttattgtattaaaagttgaaattaatatgatcactaatcaagctttctaattgttgattgtctagtgtcttctcaattcttattattatgaatatcctgataccagtttaatcttttaatgtagACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAAATTCGTAGTAAAAGAATTAAGAAAGCGGTAAAAGGAATCACTGGTAAGC
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----------------------------------------------------------cattta--gccaaaaatatt-taaatggaaatgagg--tgatactca--aaatgtttagtattt---caaatccttgcattttaa-----tttaaattgatttacttat---atgcagACTCAGCTGCGCATGGAGGCATTTTATTCATTCAATGAGAGATTTGCAAAAATTCGCAGCAAAAGGATTAAGAAAGCCATCAAGGGCATTACAGGCAAAA
upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 17
lower sequence: AT3G28030.1 (Arabidopsis thaliana), 3'ss of exon 15
gttattttgttttattgatctgctccccctttttactgactgttttatatttttattgtattaaaagttgaaattaatatgatcactaatcaagctttctaattgttgattgtctagtgtcttctcaattcttattattatgaatatcctgataccagtttaatcttttaatgtagACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAAATTCGTAGTAAAAGAATTAAGAAAGCGGTAAAAGGAATCACTGGTAAGC
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---------------------------------------------------------------------------------gtc-ttcatctaacatt-tgatctcttatcgttgatatgcttatgaataaataatatgaacagaatctgacaatttgttt--tctttccacgaagACGCAACTTCGGATTGAAGCTTTCTATTCCTTTAATGAAAGATTTGCAAAGATCCGTAGTAAAAGAATCAACAAAGCTGTCAAAGGAATTGGTGGAGGTC
upper sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv14s0066g01630.t01 (Vitis vinifera), 3'ss of exon 13
gttattttgttttattgatctgctccccctttttactgactgttttatatttttattgtattaaaagttgaaattaatatgatcactaatcaagctttctaattgtt--gattgtctagtgtcttctcaattcttat--tattatgaatatcctgataccagtttaatcttttaatgtagACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAAATTCGTAGTAAAAGAATTAAGAAAGCGGTAAAAGGAATCACTGGTAAGC
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------------------------------------------------------------------------------tttttcatttgttc--ccttctacttgtttcggtgaaagaggaagctgaacattgatatcttcttataaattatgttgttttcattggcttgattgatgaagACTCAATTGCGGTTGGAAGCATTTTACACTTTCAATGAGAGATTTGCCAAAATTCGTAGTAAGAGAATCAAAAAGGCTGTTAAAGGAATTACCGGGAGTCMapped 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|7041693|gb|AW471534.1|AW471534EST: AAGCAGATGAATTGATCCTACCAGTCTTAAAGGAGTATAACAAGCGTGAG ACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAA
genomic: AAGCAGATGAATTGATCCTACCAGTCTTAAAGGAGTATAACAAGCGTGAGgttattttgt ... tttaatgtagACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAA
EST:
gi|11688807|gb|BF596483.1|BF596483EST: AAGCAGATGAATTGATCCTACCAGTCTTAAAGGAGTATAACAAGCGTGAG ACTCAATTGCGGNTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAA
genomic: AAGCAGATGAATTGATCCTACCAGTCTTAAAGGAGTATAACAAGCGTGAGgttattttgt ... tttaatgtagACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAA
EST:
gi|19270376|gb|BM886632.1|BM886632EST: AAGCAGATGAATTGATCCTACCAGTCTTAAAGGAGTATAACAAGCGTGAG ACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAA
genomic: AAGCAGATGAATTGATCCTACCAGTCTTAAAGGAGTATAACAAGCGTGAGgttattttgt ... tttaatgtagACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctcaattcttattattatgaatatcctgataccagtttaatcttttaatgtagACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAAATTCGTAGTAAAAGAATTAAGAAAGCGGTAAAAGGAATCACTGGTAAGC
ttttaat putative branch site (score: 3)
tctttt CT-rich tract
aattcttattattatg 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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gttattttgttttattgatctgctccccctttttactgactgttttatatttttattgtattaaaagttgaaattaatatgatcactaatcaagctttctaattgttgattgtctagtgtcttctcaattcttattattatgaatatcctgataccagtttaatcttttaatgtagACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAAATTCGTAGTAAAAGAATTAAGAAAGCGGTAAAAGGAATCACTGGTAAGC
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