Sequence
atgc intronic sequence ATGC exonic sequencegtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctggtggtggtgaagtaccctcagtgtcaccactaccacaatcacctatgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTAAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G394945_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 2
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctggtggtggtgaagtaccctcagtgtcaccactaccacaatcacctatgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTAAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
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---------------------------------------------------------------------------------------------------ttttctgcattgctatggtggtgccacttgttcatcatccatcttataaaaaaagaacttgttgttcagcaaaatgatggatactatttatttgacatagGTAAGGGAGATGCCAAATGTTTTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATCACGATATTGCAGT
upper sequence: GRMZM2G394945_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctggtggtggtgaagtaccctcagtgtcaccactaccacaatcacctatgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTAAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
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-------------------------------------------------------------------------------------ctcataatcatatata----tattagattacgtctgtcagtctacaacaatgatagttttaataga---tagattatact-aacatact-----ttgtgtgtgtctgcgt-cagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
upper sequence: GRMZM2G394945_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 3
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctggtggtggtgaagtaccctcagtgtcaccactaccacaatcacctatgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTAAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT-
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--------------------------------------------------------------------------------ccact--cacaatcatatata----tatatatgtcta----tcagtctacaacaatgatagttttaataca---tagatgatgct-aacatact-----ttgtgcatgtctgcat-caggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
upper sequence: GRMZM2G394945_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctggtggtggtgaagtaccctcagtgtcaccactaccacaatcacctatgacccctcaaaatt-caagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTAAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
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-----------------------------------------------------------------------------gtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctg---ttgtttatcctgcatcca--ttatatcttgttttcattg----cagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
upper sequence: GRMZM2G394945_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S35_361V6.1 (Physcomitrella patens), 3'ss of exon 3
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctggtggtggtgaagtaccctcagtgtcaccactaccacaatcacctatgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTAAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
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------------------------------------------------------------------------gtacgtcgctatcttcaactttgcaaatcgcttcccacttccca------ctgcatggtgtttc---atttctaatgaaatcaatgcgtcgttaactaaat--gttatatttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTAAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
gactgat putative branch site (score: 3)
aaattacattttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctggtggtggtgaagtaccctcagtgtcaccactaccacaatcacctatgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTAAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA