Sequence
atgc intronic sequence ATGC exonic sequence...gttattaccacaacgttttacatgaaatatttaatcttaatcttcgggagactcaaacaccacctaagtatctaactttatttgcatgtgtgtactacagGAAGAAGGATGGGTGGTGTGCCGAGCATTCAAGAAGAGGACGGCGTATCCGGCGAGGAGCATGGTGGAGACGTGGGACTACTCCTTGCACGAGCGCAACA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g03540.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g03540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G025642_T02 (Zea mays), 3'ss of exon 3
-gttattaccacaacgttttacatgaaatatttaatcttaatcttcgggagactcaaac---accacctaagtatctaactttatttgcatgtgtgtactacagGAAGAAGGATGGGTGGTGTGCCGAGCATTCAAGAAGAGGACGGCGTATCCGGCGAGGA--GCATGGTGGAGACGTGGGACTACTCCTTGCACGAGCGCAACA
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ggagatagataggcgataatggaggcgatactgtatattgcaatcctgcacgcctcattttaacaatctaactaatcagtttaatttccgagcg----cttcagGAAGAAGGCTGGGTGGTGTGCCGAGCGTTCAAGAAGAGAACAGCGTACCCGGCAAGGATGGCATGGGGGGACCCCAG--CTACGCCTACCGCGAGATCAGCG
upper sequence: LOC_Os03g03540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G37310.1 (Glycine max), 3'ss of exon 3
gttattaccacaacgttttacatgaaatatttaatcttaatcttcgggagactcaaa----caccacctaagtatct---aacttta----tttgcatgtgtgtactacagGAAGAAGGATGGGTGGTGTGCCGAGCATTCAAGAAGAGGACGGCGTATCCGGCGAGGAGCATGG---TGGAGACGTGGGACT---ACTCCTTGCACGAGCGCAACA
||| | | || | | | ||| || ||| | ||| | | | | | ||| |||||| || ||||||| | ||||||||||||||||| |||||| |||| |||||||||| || | | ||| || || | || ||||||| || ||| | ||
----------taacatgtagcaagtc-tggtcaattcaaacagaaaggaaatacaagttatctgtattttattctctctgaactttggagcttaaattgtgtgtcatgcagGAAGAAGGATGGGTTGTGTGCAGAGCCTTCAAGAAGAAAACCACTGGGCAAACGAAGACTATTAATATTGAAGGATGGGACTCAAGCTACTTCTATGAAG------
upper sequence: LOC_Os03g03540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 2
----gtta---ttaccacaacgttttacatga-aatatttaatcttaatcttcgggagactcaaacaccacctaagtatctaactt-tatttgcatgtgtgtactacagGAAGAAGGATGGGTGGTGTGCCGAGCATTCAAGAAGAGGACGGCGTAT---CCGGCGAGGAGCATGGTGGAGACGTGGGACTACTCCTTGCACGAGCGCAACA
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cctagtcaagtcaaacataatacatttcaagagaatagagaaaccaagtccacaaaagtcttat------cttagctttccaacatgtaatcgagtgtgtgt---gcagGAGGAAGGATGGGTGGTGTGCAGAGCATTCAAGAAAAGAACAACTAACGGCCAAACGAAGACTATTGAAGGATGGCATCGAAACTGCTTATACGATG--AAC-
upper sequence: LOC_Os03g03540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G05620.1 (Glycine max), 3'ss of exon 2
gttattaccacaacgttttacatgaaatatttaatc---ttaatcttcgggagactcaaacaccaccta-agtatctaactttatttgcatgtgtgtactacagGAAGAAGGATGGGTGGTGTGCCGAGCATTCAAGAAGAGGACGGCGTATCCGGCGAGGAGCATGGTGGAGACGTGGGACT---ACTCCTTGCACGAGCGCAACA
| | | || || | |||| | || | | | || | || |||| || | || ||| | || ||||||| ||||| |||||||||||||| ||| ||||||||||||| || || | | | | | | || ||||| ||| ||| |||| |||
-tcaaacataatacattccaagagaaaagtgaaaccaattaagtccacaaaagtctcatcttagctttacaacatgtaatcgagtgtgtgtgtgtgt---gcagGAGGAAGGATGGGTGGTATGCAGAGCATTCAAGAAAAGAACAACAAACGGCCAAACAAAGACTATTGAACGATGGGATCGAAACTACTTATACGATG--AAC-
upper sequence: LOC_Os03g03540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 2
---gttattaccacaacgttttacatgaaatatttaa-tcttaatcttcgggagactcaaacaccacctaagtatctaactttatttgcatgtgtgtactacagGAAGAAGGATGGGTGGTGTGCCGAGCATTCAAGAAGAGGACGGCGTATCCGGCGAGGAGCAT----GGTGGAGACGTGGGACTACTCCTTGCACGAGCGCAACA-
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tatgctagagaaaaaaaaatttgaaaagactggaaaagtttttattttttatttttttgagt-ttatctaa-----caaattt--ctgtgtgaagcttttgcaggaagAAGGATGGGTAGTCTGCCGAGCATTCAAAAAGAGAACCACCAGCCAAAGCAAGAGCATTGAAGGGTGGGACACAAG-CTACTTCTACGATGAACCAAGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggagactcaaacaccacctaagtatctaactttatttgcatgtgtgtactacagGAAGAAGGATGGGTGGTGTGCCGAGCATTCAAGAAGAGGACGGCGTATCCGGCGAGGAGCATGGTGGAGACGTGGGACTACTCCTTGCACGAGCGCAACA
atctaac putative branch site (score: 2)
tatctaactttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttattaccacaacgttttacatgaaatatttaatcttaatcttcgggagactcaaacaccacctaagtatctaactttatttgcatgtgtgtactacagGAAGAAGGATGGGTGGTGTGCCGAGCATTCAAGAAGAGGACGGCGTATCCGGCGAGGAGCATGGTGGAGACGTGGGACTACTCCTTGCACGAGCGCAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - accacaa
- - - - - - - - -ttacatg
- - - - - - - - - - - - - - - - - - - - - - - - - actcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtg