Sequence
atgc intronic sequence ATGC exonic sequencegtaattcatgcagaactgcacaatcacccacctgttggaatagccattatgaaatgcttatttctgactaagagttctattcacagaggttatatgggtgccaagctcacaaacaacatagaatgtgaaattttccagATGCTCCTGGAGGAGGCAAGGGAGAGCTACAAAGAGGAGATAGTGATGCCCTTGCGAAGTGACAATGTGGAGGATATCAGTAGGAATGTGGGCACACTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g22950.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g22950.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G032699_T02 (Zea mays), 3'ss of exon 2
----gtaattcatgcagaactgcacaatcacccacctgttggaatagccattatgaaatgcttatttctgactaagagttctattcacagaggttatatgggtgccaagctcacaaacaacatagaatgtgaaattttccagATGCTCCTGGAGGAGGCAAGGGAGAGCTACAAAGAGGAGATAGTGATGCCCTTGCGAAGTGACAATGTGGAGGATATCAGTAGGAATGTGGGCACACTGA
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gtaggtaatccaagttgaattcgacg--taagtgcattctagtcacctcatcctgca-tccttatatttgggactaaact---tgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG----------------------------------------------------
upper sequence: LOC_Os07g22950.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G032699_T01 (Zea mays), 3'ss of exon 2
--------gtaattcatgcagaactgcacaatcacccacctgttggaatagccattatgaaatgcttatttctgactaagagttctattcacagaggttatatgggtgccaagctcacaaacaacatagaatgtgaaattttccagATGCTCCTGGAGGAGGCAAGGGAGAGCTACAAAGAGGAGATAGTGATGCCCTTGCGAAGTGACAATGTGGAGGATATCAGTAGGAATGTGGGCACACTGA
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gtaggtaggtaatccaagttgaattcgacg--taagtgcattctagtcacctcatcctgca-tccttatatttgggactaaact---tgtacagAGGTTACATGGGTTCCAAACTCGCCAACAACATAGAGTGCGAAATCTTCCAAGTGCTCCTCGAGGAGGCGAGGGAGAGCTACAGAGAGGACATCGTGATG---------------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagaggttatatgggtgccaagctcacaaacaacatagaatgtgaaattttccagATGCTCCTGGAGGAGGCAAGGGAGAGCTACAAAGAGGAGATAGTGATGCCCTTGCGAAGTGACAATGTGGAGGATATCAGTAGGAATGTGGGCACACTGA
agctcac putative branch site (score: 3)
ttttcc putative PPT
tgaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcatgcagaactgcacaatcacccacctgttggaatagccattatgaaatgcttatttctgactaagagttctattcacagaggttatatgggtgccaagctcacaaacaacatagaatgtgaaattttccagATGCTCCTGGAGGAGGCAAGGGAGAGCTACAAAGAGGAGATAGTGATGCCCTTGCGAAGTGACAATGTGGAGGATATCAGTAGGAATGTGGGCACACTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT