Sequence
atgc intronic sequence ATGC exonic sequencegtatagcttcagcttctgatgctttctattcagtttctttcaggaacaaaacacggaattacatgtcatgtctataatctaactgtatcatttgtgtcatgtctataatctaactgtatcatttgtgctcggacagCGTTTTGCTGCAGTTATCATGAGGATAAGGGACCCAAAGACAACAGCCCTGATATTTGCTTCGGGAAAGATGGTTTGCACTGGAGCAAAGAGCGAAGACC
Basic information
species | Oryza sativa |
transcript | LOC_Os10g29660.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G092916_T01 (Zea mays), 3'ss of exon 2
gtatagcttcagcttctgatgctttctattcagtttctttcaggaacaaaacacggaattacatgtcatgtctataatctaactgtatcatttgtgtcatgtctataatctaactgtatcatttgtgctcg---gacagCGTTTTGCTGCAGTTATCATGAGGATAAGGGACCCAAAGACAACAGCCCTGATATTTGCTTCGGGAAAGATGGTTTGCACTGGAGCAAAGAGCGAAGACC
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-------------------------------------------------------------------------------------ttacatttg----atatctgcagtctcagcgtgaccctgatacttacttgacagCGTTTTGCTGCGGCTATCATGAGGATAAGGGAGCCCAAGACAACGACACTGATATTTGCTTCAGGGAAGATGGTCTGCACCGGAGCAAAGAGCGAAGCCG
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G466938_T01 (Zea mays), 3'ss of exon 2
--gtatagcttcagc--ttctgatgctttctattcagtttctttcaggaacaaaacacggaattacatgtcatgtctataatctaactgtatcatttgtgtcatgtctataatctaactgtatcatttgtgctcggacagCGTTTTGCTGCAGTTATCATGAGGATAAGGGACCCAAAGACAACAGCCCTGATATTTGCTTCGGGAAAGATGGTTTGCACTGGAGCAAAGAGCGAAGACC
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gtatgtatcatcatcagtgccgctgctgccttttcatttacctt--agactttttttttg--ttgcatggaac-tatatattacattcg-atagctgcagtctcaccggcag--tgaccctgatacttactt---gacagCGTTTTGGTGCGGCTATCATGAGGATAAGGGAGCCCAAGACAACGGCACTGATATTTGCTACAGGGAAGATGGTCTGCACCGGAGCAAAGAGCGAAGCCG
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 3
gtatagcttcagcttctgatgctttctattcagtttctttcaggaacaaaacacggaattacatgtcatgtctataatctaactgtatcatttgtgtcatgtctataatctaactgtatcatttgtgctcggacagCGTTTTGCTGCAGTTATCATGAGGATAAGGGACCCAAAGACAACAGCCCTGATATTTGCTTCGGGAAAGATGGTTTGCACTGGAGCAAAGAGCGAAGACC
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----------------------------------ttttatctgagatcaataattaatttgcatgctagacatgtctttatgctg-attggtcat-ttatctgcactgctaatgtctatcatttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG----------------------------
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
gtatagcttcagcttctgatgctttctattcagtttctttcaggaacaaaacacggaattacatgtcatgtctataatctaactgtatcatttgtgtcatgtctataatctaactgtatcatttgtgctcggacagCGTTTTGCTGCAGTTATCATGAGGATAAGGGACCCAAAGACAACAGCCCTGATATTTGCTTCGGGAAAGATGGTTTGCACTGGAGCAAAGAGCGAAGACC
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----------------------------------ttttatctgagatcaataattaatttgcatgctagacatgtctttatgctg-attggtcat-ttatctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG----------------------------
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
gtatagcttcagcttctgatgctttctattcagtttctttcaggaacaaaacacggaattacatgtcatgtctataatctaactgtatcatttgtgtcatgtctataatctaactgtatcatttgtgctcggacagCGTTTTGCTGCAGTTATCATGAGGATAAGGGACCCAAAGACAACAGCCCTGATATTTGCTTCGGGAAAGATGGTTTGCACTGGAGCAAAGAGCGAAGACC
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---------------------------gatcaacatctt-----aaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatga----tgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG----------------------------
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 2
gtatagcttcagcttctgatgctttctattcagtttctttcaggaacaaaacacggaattacatgtcatgtctataatctaactgtatcatttgtgtcatgtctataatctaactgtatcatttgtgctcggacagCGTTTTGCTGCAGTTATCATGAGGATAAGGGACCCAAAGACAACAGCCCTGATATTTGCTTCGGGAAAGATGGTTTGCACTGGAGCAAAGAGCGAAGACC
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-----------------------------------------------------------------------------------------gtttgtggga-gagaggaagttttctaacttaacgctctggaaacagCGTTTCGCAGCCGTGATCATGAGAATAAGGGAGCCCAAGACGACAGCGCTGATTTTTGCGTCGGGAAAGATG---------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgtatcatttgtgtcatgtctataatctaactgtatcatttgtgctcggacagCGTTTTGCTGCAGTTATCATGAGGATAAGGGACCCAAAGACAACAGCCCTGATATTTGCTTCGGGAAAGATGGTTTGCACTGGAGCAAAGAGCGAAGACC
atctaac putative branch site (score: 2)
tataatctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagcttcagcttctgatgctttctattcagtttctttcaggaacaaaacacggaattacatgtcatgtctataatctaactgtatcatttgtgtcatgtctataatctaactgtatcatttgtgctcggacagCGTTTTGCTGCAGTTATCATGAGGATAAGGGACCCAAAGACAACAGCCCTGATATTTGCTTCGGGAAAGATGGTTTGCACTGGAGCAAAGAGCGAAGACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA