Sequence
atgc intronic sequence ATGC exonic sequence...ctgatgcaatttaatgcaaccgattgtttattttttgtatgcttgaatgcttccattttagttgcgttttgaatttactgaaatagtatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGATGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTACGTGACC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G863698_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 7
ctgatgcaatttaatgcaaccgattgtttattttttgtatgcttgaatgcttccattttagttgcgt--tttgaatttactg-aaatagtatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGATGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTACGTGACC
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--cttttgatgctatataaacaattttgccttatttctatgtgggtaagctcattttgttgttacgtaacttatatttgctgcaaacaatatatgaat-acagGTTCAGGAGCCAGACTTAGTTGGTGTAAGCCATTTACTAGTTGATGAAATTCATGAACGTGGCATGAATGAAGATTTTCTCATCATAATTCTTCGCGACC
upper sequence: GRMZM5G863698_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G35240.1 (Glycine max), 3'ss of exon 8
-ctgatgca-atttaatgcaaccgattgtttattttttgtatgcttgaatgcttccattttagttgcg-ttttgaatttactgaaatagtatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGATGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTACGTGACC
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aaaaatatatagttgagaattttgcatctttatatgggatgttcttatattcttcctagcaactagtggccttgtttttactgtctttgttgttaaat---agGTACAAGACCCAGACTTGACTGGTGTTAGTCATTTGCTGGTGGATGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC
upper sequence: GRMZM5G863698_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 6
-ctgatgca-atttaatgcaaccgattgtttattttttgtatgcttgaatgcttccattttagttgcg-ttttgaatttactgaaatagtatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGATGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTACGTGACC
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aaaaatatatagttgagaattttgtatccgtatatgaaattttcttatattcttcctagcaactagtggccttgtttttattgtctttgttgttaaat---agGTACAAGACCCAGACTTGATAGGTGTTAGTCATTTGCTGGTGGACGAAATTCATGAAAGAGGCATGAATGAAGACTTTTTAATTATAATTTTACGTGACC
upper sequence: GRMZM5G863698_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 6
ctgatgcaatttaatgcaaccgattgtttattttttgtatgcttgaatgcttc---catttta--gttgcgttttgaatttactga--aatagtatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGATGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTACGTGACC
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----tgtcatttgaag-gattagttgttg--tataagcatactgggatggcacacacattctgatgttttcttttccattctcttatgattttgatgttaaatacagGTTCAGGACCCAGATCTAACTGGTGTAAGCCATTTGCTAGTGGATGAAATTCATGAAAGAGGCATGAATGAGGACTTCCTTTTAATAATTTTGCATGACC
upper sequence: GRMZM5G863698_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S36_206V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------------ctgatgcaatttaatgcaaccgattgtttattttttgtatgcttgaatgcttccattttagttgcgttttgaatttactgaaatagtatataaa-ttgca--gGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGATGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTACGTGACC
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gtacgttctgtgccttatattacgaacttggagattctttttcattgtatgattgtctagtacttggcagaaatttgcagtgcagaagatcaatggtaggtaggaaccacttc-gtcatttgccagtactaacttgttggcatgtggggttgcatagGTCCAAGAGCCTGACTTGAATGGTGTGAGTCATGTCATGGTTGACGAAATTCATGAACGCGGCATGAATGAAGATTTCTTATTGATCATTTTACGAGATC
upper sequence: GRMZM5G863698_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S65_202V6.1 (Physcomitrella patens), 3'ss of exon 1
ctgatgcaatttaatgcaaccgattgtttattttttgtatgcttgaatgcttccattttagttgcgttttgaatttactgaaatagtatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGATGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTACGTGACC
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------------------------------------------gtgagttgcccattcttagtcac---ttgtatttcctgg---------tgaat---agGTCCAGGAGCCTGACTTGAATGGTGTGAGTCACATTATGGTTGACGAGATTCATGAACGCAACATGAATGAAGATTTTCTGCTGATCATTTTTCGGGACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgcttccattttagttgcgttttgaatttactgaaatagtatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGATGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTACGTGACC
ttttgaatttactgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgatgcaatttaatgcaaccgattgtttattttttgtatgcttgaatgcttccattttagttgcgttttgaatttactgaaatagtatataaattgcagGTTCAAGAGCCTGACTTAATTGGGGTGAGTCATTTACTAGTTGATGAAATTCATGAACGCGGCATGAATGAAGATTTTCTCATCATAATACTACGTGACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
ctgatgc
- - - - - - aatgcaa
- - - - - - - - - - - - - - - - - -tgtatgc
- - - - - - - - - - - - - - - - - - - - - ttgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttactg
