Sequence
atgc intronic sequence ATGC exonic sequencegtgagctatctcccttcctcgtcatctttcgttctgcggatatgaaaccgttggttctgacccgtcccttggtgtggccacatctcttttgtgcagTGTGGATCCATTCAGCAAGAAGGACCGGTATGATATCAAGGCTCCGCCAGTCTTCAGCGTGCGCAACATCGGCAAGACCCTGGTGTCCAGGACACAGGGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G703354_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g10340.1 (Oryza sativa), 3'ss of exon 1
gtgagctatctccc---------ttcctcgtcatctttcgttctgcggatatgaaaccgttggttctgacccg----tccct---tgg--tgtggccacatctct----tttgtgcagTGTGGATCCATTCAGCAAGAAGGACCGGTATGATATCAAGGCTCCGCCAGTCTTCAGCGTGCGCAACATCGGCAAGACCCTGGTGTCCAGGACACAGGGC
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gtgagtgccctcctgcccaccgttctctcctcctcctcctgcttagagatccaaaccccttcatttttactcgctagtcgctacatgggttgttgatgcagctttgcatttcttgcagCGTCGATCCCTTTGCTAAGAAGGACTGGTATGATATCAAGGCCCCGTCGGTGTTCAATGTGCGGAACATCGGCAAGACCCTCGTGTCCAGGACACAGGGT
upper sequence: GRMZM2G703354_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g21798.1 (Oryza sativa), 3'ss of exon 1
gtgagct-atctcccttcctcg---tcatctttcgttctgcggatatgaaacc--gttggttctgacccgtc--ccttggtgtggccacatc--------tcttttgtgcagTGTGGATCCATTCAGCAAGAAGGACCGGTATGATATCAAGGCTCCGCCAGTCTTCAGCGTGCGCAACATCGGCAAGACCCTGGTGTCCAGGACACAGGGC
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gtgagtttacctctcccccccaccctcctcgtccgtccttcttcctttcgctcttggttgccatggcgcatgggtgttgatgtggcttcctgctcgttcgtttttcttgcagCGTCGATCCTTTTGCGAAGAAGGATTGGTATGATATCAAGGCCCCGTCGGTGTTCAACGTGAGAAACGTCGGGAAGACGCTCGTGTCCAGGACACAGGGC
upper sequence: GRMZM2G703354_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S17_306V6.1 (Physcomitrella patens), 3'ss of exon 1
---------gtgagctatctcccttcctcgtcatctttcgttctgcggatatgaaaccgttggttctgacccgtccct--tggtgtggccacatctcttt--tgtgcagTGTGGATCCATTCAGCAAGAAGGACCGGTATGATATCAAGGCTCCGCCAGTCTTCA-GCGTGCGCAACATCGGCAAGACCCTGGTGTCCAGGACACAGGGC
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gtaacgtccgctggctgtctgagctctttacgacagtcgaatgtgtaatttcatttttgtgagttattgagggtttctgctaacttgacgacgtgggagtggtgtgcagTGTCGACCCCTTCTCCAAGAAGGACTGGTATGATATCAAGGCTCCTAACACCTTCACGCAGAAGTCGC-TTGGGAAGACCCTTGTCACCAGAACCGCGGGT
upper sequence: GRMZM2G703354_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S92_47V6.2 (Physcomitrella patens), 3'ss of exon 1
--gtgagctatctcccttcctcgtcatctttcgttctgcggatatgaaaccgttg-----gttctgacccgtcccttggtgtggccacatctcttttgtgcagTGTGGATCCATTCAGCAAGAAGGACCGGTATGATATCAAGGCTCCGCCAGTCTTCAGCGTGCGCAACATCGGCAA-GACCCTGGTGTCCAGGACACAGGGC
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gtacgtctaaattcaacatggcgttgtgaggtttttggtgggtttttgtgggttgtgagcatttaaaactgtcatattgattttttttgtgcgtcttgtgcagTGTCGATCCTTTCTCCAAGAAGGACTGGTATGATATCAAGGCACCCAATATCTTCA-CGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaaaccgttggttctgacccgtcccttggtgtggccacatctcttttgtgcagTGTGGATCCATTCAGCAAGAAGGACCGGTATGATATCAAGGCTCCGCCAGTCTTCAGCGTGCGCAACATCGGCAAGACCCTGGTGTCCAGGACACAGGGC
ttctgac putative branch site (score: 2)
catctctttt putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagctatctcccttcctcgtcatctttcgttctgcggatatgaaaccgttggttctgacccgtcccttggtgtggccacatctcttttgtgcagTGTGGATCCATTCAGCAAGAAGGACCGGTATGATATCAAGGCTCCGCCAGTCTTCAGCGTGCGCAACATCGGCAAGACCCTGGTGTCCAGGACACAGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA