Sequence
atgc intronic sequence ATGC exonic sequence...ccattgcattaggcctactatttgatgtttaaaatataaatctttataaaatagagctcatggggcattaatttgtcatttctactgtattatcaaacagGCAACGCTGAATGTTTGGGGACAGAACTTTTGGAGACTTTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTCAGACTACGAGATTATAATGGTGACGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G075921_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g10680.1 (Oryza sativa), 3'ss of exon 2
-----ccattgcattaggcctactatttgatgtttaaaatataaatctttataaaatagagctcatggggcattaatttgtcatttctactgtattatcaaacagGCAACGCTGAATGTTTGGGGACAGAACTTTTGGAGACTTTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTCAGACTACGAGATTATAATGGTGACGC
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ttttttcattgcggcatactgtaaatctgtaatttagtatgcca-tctctacatgagggtgtccagtgaatatg----tgtaatttctattgttcttttgagcagGCAATGCTGAATGCCTGGGGAGTGAACTTTTGGAAACATTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTGAAACTACGAGACTACAGTGGTGACTT
upper sequence: GRMZM2G075921_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G05220.1 (Glycine max), 3'ss of exon 2
--ccattgcattaggcctactatttgatgtttaaaatataaatctttataaaatagagctcatggggcattaatttgtcatttctactgtattatcaaacagGCAACGCTGAATGTTTGGGGACAGAACTTTTGGAGACTTTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTCAGACTACGAGATTATAATGGTGACGC
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gtctattgt-ttgtttttacc-ttgaactcttgaaccaattgcttatctacattctgtattttcactttgctaatcggggttattatttttggatgaaatagGGAATCCTGAAGGCTTGGGCACTGAGCTGTTGGAAACCCTAGTAAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTCAAAAACTATGATGGTGATCT
upper sequence: GRMZM2G075921_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G40080.1 (Glycine max), 3'ss of exon 2
ccattgcattaggcctactatttgatgtt----taaaatataaatctttataaaata-gagctcatggggcattaatttgtcatttctactgtattatcaaacagGCAACGCTGAATGTTTGGGGACAGAACTTTTGGAGACTTTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTCAGACTACGAGATTATAATGGTGACGC
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-----ttgacatgtctattgtttgtttttaccttgaaccaattgcttatctacattctgtattttcactttgctaaccgggggtgttattttttttatgaaacagGGAATCCTGAAGGTTTGGGCACTGAGCTATTGGAAACCCTAGTGAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTTAAAAACTATGACGGCGATCT
upper sequence: GRMZM2G075921_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0129g00220.t01 (Vitis vinifera), 3'ss of exon 2
ccattgcattaggcctactat---ttgatgtttaaaatataaat-ctttataaaatagagctcatggggcattaatttgtcatttctactgtattatcaaacagGCAACGCTGAATGTTTGGGGACAGAACTTTTGGAGACTTTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTCAGACTACGAGATTATAATGGTGACGC
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gaattaaaacagattatatgtccattaatgttcatttaatgcttgctttgcaaataattgtttgtggggatcctaagtgaaatattt-ttgt-ctgt--ggcagGTAACCCAGAAAGCTTGGGTGCTGAGCTTTTGGAAACTTTAGTAAAGATGGCTCCCACCAAGGAGGAAGAAATAAAACTTCGAGATTACAGTGGTGACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaaatagagctcatggggcattaatttgtcatttctactgtattatcaaacagGCAACGCTGAATGTTTGGGGACAGAACTTTTGGAGACTTTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTCAGACTACGAGATTATAATGGTGACGC
cattaat putative branch site (score: 3)
attaatttgtcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccattgcattaggcctactatttgatgtttaaaatataaatctttataaaatagagctcatggggcattaatttgtcatttctactgtattatcaaacagGCAACGCTGAATGTTTGGGGACAGAACTTTTGGAGACTTTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTCAGACTACGAGATTATAATGGTGACGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- -ttgcatt
- - - - - - - - - - - tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gctcatg