Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcgtcatcagttgactctgccccctgtgttcttttcctcaacgttaacagcatttgtgtttttgagcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g50750.3 (Oryza sativa), 3'ss of exon 10
------------------------------------------------------------------------gtaa-gtcgtcatcagttgactctgccccctgt---gttcttttcctcaacgttaacagcatttgtgtttttgagcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
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gtaagtttagtattcagtatttcagttccttgtgccctttgttctacgaattcatagcttgctaccaagactgtaaagctactatttgttctttgtgaccattgcaaagtctaaagttttaaccctgtctg--ttcttcttactgaacagGAAATTCCAGATAACGAGTTTGAGAAGCGCATCAGGCCAGAGGTTATACCAGCCAGTGAGATAGGAGTGACTTTTGATGACATTGGAGCCCTGGCTGACA
upper sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA09G23250.1 (Glycine max), 3'ss of exon 10
---------------------------gtaagtcgtcatcagttgactctgccccctgtgttcttttcctcaacgtta-acagcatttgtgtttttgagcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
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ctagccatgtaactgaagctgtgtgatataaattctaaacttatttccttttactttgcccccttttttgtgttactatatactaattgcttgctt--gcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCGTTGGATGAGA
upper sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 10
---------------------gtaagtcgtcatcagttgactctgccccctgtgttcttttcctca---acgttaacagcatttgtgtttttga--gcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
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actagccatgcagctgaagctgtatgatttaaattctaaacttatttccttttactttcccccttttttgtgttactatatactaatttcttgcttgcagGAAGTTCCTGACAACGAGTTTGAGAAGCGCATAAGACCAGAGGTTATCCCTGCAAATGAGATAGGGGTTACATTTGCAGATATTGGTGCATTGGATGAGA
upper sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv02s0025g00650.t01 (Vitis vinifera), 3'ss of exon 11
-------------------gtaagtcgtcatcagttgactctgccccctgtgttcttttc-----ctcaacgttaacagcatt--tgtgtttttg-agcagGAAGTTCCA---GACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
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tttgtttaatttacaaaaaataatctgtt-tcaatcgcatttgattttcttaccttttttgtagttttaacgttgaaaggcctgctatattttcctaacagGAAGTTCCTCCTGACAATGAATTTGAGAAGCGCATCAGACCAGAGGTCATCCCAGCTAGTGAGATTGGTGTGACATTTGCTGATATTGGTGCCATGGATG---
upper sequence: GRMZM2G128748_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 12
-------------------------gtaagtcgtcatcagttgactctgccccctgtgttcttttcctcaacgttaacagcatttgt-gtttttgagcagGAAGTTCCA---GACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
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gatcacaatgctgatttttgtaaaagaaaattttattgggaaaattttccatcattcccttactcttttaactgttgaactgttaattgtttccctccagGAAGTTCCACCTGACAATGAATTTGAGAAGCGTATAAGGCCAGAGGTTATCCCAGCGAATGAGATAGGAGTGACATTTGATGATATCGGTGCTTTGAGTG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctgccccctgtgttcttttcctcaacgttaacagcatttgtgtttttgagcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
cgttaac putative branch site (score: 3)
tgttttt putative PPT
ttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcgtcatcagttgactctgccccctgtgttcttttcctcaacgttaacagcatttgtgtttttgagcagGAAGTTCCAGACAATGAGTTTGAAAAGCGTATCAGACCAGAGGTCATTCCGGCAAGTGAGATAGGAGTGACATTCGATGACATCGGAGCCCTGGCAGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT