Sequence
atgc intronic sequence ATGC exonic sequence...atgcataatcccctattgcatcttgtgtatgcataatcctccgatatacatttcgatgatgctaaaggactaaattcatctgagcttatgcattgtgcagTGAGATCAAGGAACGCATCAAGAAGACCAAGGATGAAAAGAAGGCGAAGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g40820.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g40820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G142640_T03 (Zea mays), 3'ss of exon 4
atgcataatcccctattgcatcttgtgtatgcataatcctccgatatacatttcgatgatgctaaaggactaaattcatctgagcttatgc-attgtgcagTGAGATCAAGGAACGCATCAAGAAGACCAAGGATGAAAAGAAGGCGAAGAAG------------------------------------------------
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------------gtatgtctgccagt-tctatattaccataacaaatagataccgatgct-caatacctctccgctcatttgaactgtcgtgaccatgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAAGCGAAGAAGGCGGAGGTGAGCAAGTCCCAGAAGACGCAGACAAAGGGTGCGGTCCAG
upper sequence: LOC_Os05g40820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G110328_T04 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------atgcataatcccctattgcatcttgtgtatgcataatcct---ccgatatacattt--cgatgatgctaaaggactaaattcatctgagcttatgca-----ttgtgcagTGAGATCAAGGAACGCATCAAGAAGACCAAGGATGAAAAGAAGGCGAAGAAG------------------------------------------------
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gtatgcttgtcgattttataataaaataaagccatcatttgtgcctatgacagtggtaactgtctgttggcctaaccaacaaaatctctgagtgacatttaacagaaacacaatagatacagatgcttgat-atcaggctcatttgaacacccactgacacctttgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAAAAGGCTGAGGTGACCAAGTCCCAGAAGGCACAGACGAAGGGAGCGGTCCAG
upper sequence: LOC_Os05g40820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G074898_T01 (Zea mays), 3'ss of exon 5
------------------------------------atgcataatcccctattgcatcttgtgtatgcataatcctccgatatacatttcgatgatgctaaaggactaaattcatctgagcttatgc--attgtgcagTGAGATCAAGGAACGCATCAAGAAGACCAAGGATGAAAAGAAGGCGAAGAAG------------------------------------------------
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gtaatgtttacatcctccatttatatgcctatgacagcagctaaccatctgtttggtgttgccaataaaatctgttttgctctcgagtgttactgtacacaaacgtgcaatacatttgaactgccgctgaccttacagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAGGCGAAGAAGGCTGAGGTGTCCAAGTCCCAGAAGGCGCAGACGAAGGGTGCTGTTCAG
upper sequence: LOC_Os05g40820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G53020.1 (Arabidopsis thaliana), 3'ss of exon 4
atgcataatcccctattgcatcttgtgtatgcataatcctccgatatacatttcgatgatgctaaaggactaaattcat---ctgagcttatg---cattgtgcagTGAGATCAAGGAACGCATCAAGAAGACCAAGGATGAAAAGAAGGCGAAGAAG------------------------------------------------
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-------------gttagttttctccctctgtcaaatcatccaactaggattaaaatagttatatttgacttaataaatgtattgtgatgatgattcaacaaacagTGAGATCAAGGAAAGAATCAAAAAGACCAAAGATGAAAAGAAGGCTAAGAAGGTGGAATTTGCTTCTAAGCAACAGAAGGTCAAGGCTAATTTCCCCAAA
upper sequence: LOC_Os05g40820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G36620.1 (Arabidopsis thaliana), 3'ss of exon 4
--atgcataatcccctattgcatcttgtgtatgcataatcctccgatatacatttcgatgatgctaaaggactaaattcatctgagcttatgcattgtgcagTGAGATCAAGGAACGCATCAAGAAGACCAAGGATGAAAAGAAGGCGAAGAAG------------------------------------------------
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gtttgtttctttcccgaagacagtcactatatacatcaatttttttttgaaactgaaatg----tgattgattcaa---agctaatctgatg-attatgcagTGAGATCAAGGAGAGAATCAAGAAGACCAAGGACGAGAAGAAGGCAAAGAAGGTCGAGTATGCATCAAAGCAACAGAAGTCACAAGTGAAGGGAAATATCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|88397656|gb|CI684589.1|CI684589EST: AGAGCTGAAAAGCCTGAAGTTCGTGATGCTGCTAGAGAAGCTGCTCTTCG TGAGATCAAGGAACGCATCAAGAAGACCAAGGATGA
genomic: AGAGCTGAAAAGCCTGAAGTTCGTGATGCTGCTAGAGAAGCTGCTCTTCGgtatgctctt ... cattgtgcagTGAGATCAAGGAACGCATCAAGAAGACCAAGGATGA
EST:
gi|86417460|gb|CI031669.1|CI031669EST: AGAGCTGAAAAGCCTGAAGTTCGTGATGCTGCTAGAGAAGCTGCTCTTCG TGAGATCAAGGAACGCATCAAGAAGACCAAGGATGAAAAGAAGGCGAAGAA
genomic: AGAGCTGAAAAGCCTGAAGTTCGTGATGCTGCTAGAGAAGCTGCTCTTCGgtatgctctt ... cattgtgcagTGAGATCAAGGAACGCATCAAGAAGACCAAGGATGAAAAGAAGGCGAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacatttcgatgatgctaaaggactaaattcatctgagcttatgcattgtgcagTGAGATCAAGGAACGCATCAAGAAGACCAAGGATGAAAAGAAGGCGAAGAAG
gactaaa putative branch site (score: 2)
taaattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgcataatcccctattgcatcttgtgtatgcataatcctccgatatacatttcgatgatgctaaaggactaaattcatctgagcttatgcattgtgcagTGAGATCAAGGAACGCATCAAGAAGACCAAGGATGAAAAGAAGGCGAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG