Sequence
atgc intronic sequence ATGC exonic sequence...atgccttaagaattgttcctgttgtgtttacatctaatgaacattttagaatgtaagtcgaaggagttggttataacacgttgtgatgtatgcgttgcagGTAAGATGCCTCTACATCAAGAGCACCATGGGGAAACCATGCAGGGTGTTCTAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os08g44450.3 (Oryza sativa), 3'ss of exon 2
---------------------------------------------------------------atgccttaagaat-tgttcctgttgtgtttacatctaatgaacattttagaatgtaagtcgaaggagttggttataacacgttgtgatgtatgcgttgcagGTAAGATGCCTCTACATCAAGAGCACCATGGGGAAACCATGCAGGGTGTTCTAA----------------------------------------------
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gtgagttatctgttctgagcctgtttgcatgcaattaaacttacagctcaaatctgtttaacaacatagtgaatatatatgagttttggccttgctttgaataatagtttta---tgtgag--aaaacaactgatgataacttggaattgtttgtgtttgatagGTGAGGTGCCTTTACATCAAGAGCACCATGGGGAAACCAATCAGGGTGTTCTAAGTTGGTGTGTTCCACCTAGAAGTGAAAAGGATCAGTTGAAACCAAG
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os08g44450.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------------atgccttaagaat-tgttcctgttgtgtttacatctaatgaacattttagaatgtaagtcgaaggagttggttataacacgttgtgatgtatgcgttgcagGTAAGATGCCTCTACATCAAGAGCACCATGGGGAAACCATGCAGGGTGTTCTAA---------------------------------------------------
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gttatctgttctgagcctgtttgcatgcaattaaacttacagctcaaatctgtttaacaacatagtgaatatatatgagttttggccttgctttgaataatagtttta---tgtgag--aaaacaactgatgataacttggaattgtttgtgtttgataggtgagGTGCCTTTACATCAAGAGCACCATGGGGAAACCAATCAGGGTGTTCTAAGTTGGTGTGTTCCACCTAGAAGTGAAAAGGATCAGTTGAAACCAAGCTTTT
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os08g44380.2 (Oryza sativa), 3'ss of exon 5
---------------------atgccttaagaa--ttgttcctgttgtgtttacatctaatgaacattttagaatgtaagtcgaaggagt--------tggttataacacgttgtgatgtatgcgttgcagGTAAGATGCCTCTACATCAAGAGCACCATGGGGAAACCATGCAGGGTGTTCTAA----------------------------------------------
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gtgagttctgttctcaacttcatggcatcagtagtttacatttctgatgtttacatgtaatgaaatttatatagtgtaagcccaacaagcaaacacaatcagtctaacttgttatggtttgtgctttgcagGTGAGGTGCCTGTACATCAAAAGCACAATGGGGAAACCGTACAGGGTGTTCTAAGCTGGTTTGCTCCACATTGAAGCTGATAAGATGCTGGGCGGTTGAA
upper sequence: GRMZM5G862017_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os08g44380.1 (Oryza sativa), 3'ss of exon 5
-----------------atgccttaagaa--ttgttcctgttgtgtttacatctaatgaacattttagaatgtaagtcgaaggagttggt--------tataacacgttgtgatgtatgcgttgcagGTAAGATGCCTCTACATCAAGAGCACCATGGGGAAACCATGCAGGGTGTTCTAA---------------------------------------------------
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gttctgttctcaacttcatggcatcagtagtttacatttctgatgtttacatgtaatgaaatttatatagtgtaagcccaacaagcaaacacaatcagtctaacttgttatggtttgtgctttgcaggtgagGTGCCTGTACATCAAAAGCACAATGGGGAAACCGTACAGGGTGTTCTAAGCTGGTTTGCTCCACATTGAAGCTGATAAGATGCTGGGCGGTTGAACTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagaatgtaagtcgaaggagttggttataacacgttgtgatgtatgcgttgcagGTAAGATGCCTCTACATCAAGAGCACCATGGGGAAACCATGCAGGGTGTTCTAA
ttataac putative branch site (score: 2)
ttataaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgccttaagaattgttcctgttgtgtttacatctaatgaacattttagaatgtaagtcgaaggagttggttataacacgttgtgatgtatgcgttgcagGTAAGATGCCTCTACATCAAGAGCACCATGGGGAAACCATGCAGGGTGTTCTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
-tgcctta
- - - - - - - - -cctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgatg