Sequence
atgc intronic sequence ATGC exonic sequence...ccgctttaaaaaccatggtcaagcttgaaatatctcatcaccacttgatggctgtcccctttaattctttacaatattttgtatacaaatgtaaatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAGTGCCTTCACTAACCTGTATGACTTGATGATGGAACTTGTTGACGTTTAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 3'ss of exon 5
ccgctttaa----aaaccatggtcaagct---tgaaatatctcatcaccacttgatggctgtcccctttaattctttacaatattttgtatacaaatgtaaatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAGTGCCTTCACTAACCTGTATGACTTGATGATGGAACTTGTTGACGTTTAC
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---ctttgagttcatgtcatgtataagatgtcttaaatatgtgatctttgcgtaacgg--atccatcccaattcatt-cgttgttttgtgaactaatgtaa-tacagCCTACTCTATGGAGCAGAAGATTCCTCGATTGCTGGAATGGTATTGGATAGTGCTTTCACTAACTTATATGGCTTGATGATGGAGCTTGTGGATGTCTAC
upper sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 4
ccgctttaaaaaccatggtcaagcttgaaatatctcatcaccacttg-atggctgtcccctttaattctttacaatattttgtatacaaatgta-aatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAGTGCCTTCACTAACCTGTATGACTTGATGATGGAACTTGTTGACGTTTAC
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-tgttaaaatatacctcatcta-ttctatgtgtgtaattataagtcacatatatgagaatctctagtatagttatttctcactttgctttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTAATGATGGAGCTTGCTGATGTCTAT
upper sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 6
-ccgctttaaaaaccatggtcaagcttgaaatatctcatcaccacttgatggctgtcccc--tttaattctttacaatattttgtatacaaatgtaaatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAGTGCCTTCACTAACCTGTATGACTTGATGATGGAACTTGTTGACGTTTAC
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atggtcttacctttactctgtatacatgtaattatgagccacccttatattcacaactctagtttaattgtctat--tcccttttactttggtgtga-tgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
upper sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 6
ccgctttaaaaaccatggtcaagcttgaaatatctcatcaccacttgatggctgtcccctttaattctttacaatatt---ttgtatacaaatgtaaatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAGTGCCTTCACTAACCTGTATGACTTGATGATGGAACTTGTTGACGTTTAC
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--atggtcctacctttactccgtatataagtaattattagccacccatatattcaaatttctagtttaattgactattcccttttactttggtgtga-tgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
upper sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 6
ccgctttaaaaaccatggtcaagcttgaaatatctcatcaccacttg-----atggctgtcccc--tttaattctttacaatattttgtatacaaatgtaaatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAGTGCCTTCACTAACCTGTATGACTTGATGATGGAACTTGTTGACGTTTAC
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--gttaaaatatctctcatct-gttccatatgtgttattgtaagtcacatatatgagaatctctagtgtaatttatttctcacttttcttt---ggtgcgg-tgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTGATGATGGAGCTTGCTGATGTCTATMapped 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|148969598|gb|EE020437.2|EE020437EST: CAAGTTTCCACTATAGGCCTTTGGGGGCGATCAATGGGTGCCGTTACATG CCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAG
genomic: CAAGTTTCCACTATAGGCCTTTGGGGGCGATCAATGGGTGCCGTTACATGgtaattggta ... gtaaatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatggctgtcccctttaattctttacaatattttgtatacaaatgtaaatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAGTGCCTTCACTAACCTGTATGACTTGATGATGGAACTTGTTGACGTTTAC
ctttaat putative branch site (score: 4)
tttaattctttacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccgctttaaaaaccatggtcaagcttgaaatatctcatcaccacttgatggctgtcccctttaattctttacaatattttgtatacaaatgtaaatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAGTGCCTTCACTAACCTGTATGACTTGATGATGGAACTTGTTGACGTTTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA