Sequence
atgc intronic sequence ATGC exonic sequence...aggatttatagtgttgattggtttttgaaatttgactttatttgtatgtcaaccatttttctgtcaaagtttgagaatattgagatccttacttttacagGGGCGCCTCTTCTTTTCACCAAGAATTATTGGATTTTATTCCAACATATTTGGTCACAAGACCAAGTTTTTCTTTTTGTGGGATGATGTTGACGATATCC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g40570.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g40570.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G372877_T01 (Zea mays), 3'ss of exon 5
aggatttatagtgttgattggtttttgaaatttgactttatttgtatgtcaaccatttttctgtcaaagtttgagaatattgagatccttacttttacagGGGCGCCTCTTCTTTTCACCAAGAATTATTGGATTTTATTCCAACATATTTGGTCACAAGACCAAGTTTTTCTTTTTGTGGGATGATGTTGACGATATCC
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------------gttgat-ggttcgt----ttggctcctgccggtgtccaaccccccgttgtgttggcactaaaaacctgtcccgtttcatgtgatgcagGGCCGCCTCTTTTTCTCCCCGAGAATAGTTGGGTTTTATTCCAACATATTTGGGCACAAGACCAAGTTCTTCTTTCTGTGGGAGGACGTCGACGACATCC
upper sequence: LOC_Os06g40570.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S26_247V6.1 (Physcomitrella patens), 3'ss of exon 10
aggatttatagtgttgattggtttttgaaatttgactttatttg---tatgtcaaccatttttctgt---caaagtttgagaatattgagatccttactttta-cagGGGCGCCTCTTCTTTTCACCAAGAATTATTGGATTTTATTCCAACATATTTGGTCACAAGACCAAGTTTTTCTTTTTGTGGGATGATGTTGACGATATCC
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----tttgtatt--cgtccggtttcataggagcaccatttttcaatctgtttcaaaaatgtttctgattgctgaacttgtgc-tgtcgataatcgttcgtgcatcagGGGCGCTTGTTCTTGTCTGTACGTTTACTGGGGTTTTACTCCAACTTATTTGGTCACAAGACCAAGTTCACCATCCTCTGGGAGGACATTGAAGAAATAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtcaaccatttttctgtcaaagtttgagaatattgagatccttacttttacagGGGCGCCTCTTCTTTTCACCAAGAATTATTGGATTTTATTCCAACATATTTGGTCACAAGACCAAGTTTTTCTTTTTGTGGGATGATGTTGACGATATCC
tccttac putative branch site (score: 2)
tccttactttt CT-rich tract
ttactttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggatttatagtgttgattggtttttgaaatttgactttatttgtatgtcaaccatttttctgtcaaagtttgagaatattgagatccttacttttacagGGGCGCCTCTTCTTTTCACCAAGAATTATTGGATTTTATTCCAACATATTTGGTCACAAGACCAAGTTTTTCTTTTTGTGGGATGATGTTGACGATATCC
- - - - - -tgttgat
- - - - - - - - - - gtttttg
- - - - - - - - - - - - - - - - - - - - -ttgtatg