Sequence
atgc intronic sequence ATGC exonic sequence...tcttgccgaaatatcattttcagtgcttcttgcatgggttttttttggattagttacttattgagataatttctttgttttggtgcttcatattttgcagGGTAATGGGTGCTGCTGCTCTTCAAAAGTATATTGGTAGCTTAGGTGGAATAGGGGCATCTGGTGTTGGTTCCAGTTCATCATATTCTCCTAAAGAATTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g43150.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 4
tcttgccgaaatatcattttcagtg-cttcttgcatgggttttttttggattagttacttattgagataatttctttgtt--ttggtgcttcatattttg---cagGGTAATGGGTGCTGCTGCTCTTCAAAAGTATATTGGTAGCTTAGGTGGAATAGGGGCATCTGGTGTTGGTTCCAGTTCATCATATTCTCCTAAAGAATTG
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------aggagaaccactatcaaagactacctggtttcgttgcaaccataaacaccatttacccaaaatgttttttcgatgctcactgcataatattttgttccagGGTGATGGGTGCTGCTGCACTTCAAAAGTATATTGGGAGCTTAGGTGGAATTGGGGCATCTGGTGTTGGTTCTAGCTCATCATATTCTCCAAAAGAGATG
upper sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 4
tcttgccgaaat--atcattttcagtgcttcttgcatgggttttttttggattagttacttattgagataatttctttgt-----tttggtgcttcatattttg---cagGGTAATGGGTGCTGCTGCTCTTCAAAAGTATATTGGTAGCTTAGGTGGAATAGGGGCATCTGGTGTTGGTTCCAGTTCATCATATTCTCCTAAAGAATTG
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------tgaaatgaataattttcttaatatgttaatt--gtttgggccaaacttggtatatgtttaaat--ttgctttgtggatgctcactgcataatatcttgttccagGGTGATGGGTGCTGCTGCACTTCAAAAATATATTGGGAGCTTAGGTGGAATTGGGGCATCTGGTGCTGGTTCTAGCTCATCATATTCTCCAAAAGAGATG
upper sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 4
--tcttgccgaaatatcattttcagtgcttcttgcatgggttttttt-tggattagttacttattgagataatttctttgttttggtgcttcatattttgcagGGTAATGGGTGCTGCTGCTCTTCAAAAGTATATTGGTAGCTTAGGTGGAATAGGGGCATCTGGTGTTGGTTCCAGTTCATCATATTCTCCTAAAGAATTG
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aatcaagtcta--ttgcactgtcactcacactcatgcaggtttatgtgctccctgactgattactgtttccgtttctattattaattgaatattacttt-cagGGTAATGGGTGCTGCTGCACTCCAGAAGTACATAGGTAGCTTAGGTGGGATAGGTGCATCAGGTGTTGGCTCAAGCTCTTCCTATGCGCCTAAAGAGTTAMapped 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|29635150|gb|CB640159.1|CB640159EST: CAAGAAATCTTCTCGACTGTGCTGTTTACAATTGCTGTTGGACTAATGTG GGTAATGGGTGCTGCTGCTCTTCAAA-GTATATTGGTAGC
genomic: CAAGAAATCTTCTCGACTGTGCTGTTTACAATTGCTGTTGGACTAATGTGgtatgttcaa ... tattttgcagGGTAATGGGTGCTGCTGCTCTTCAAAAGTATATTGGTAGC
EST:
gi|29672102|gb|CB668377.1|CB668377EST: CAAGAAATCTTCTCGACTGTGCTGTTTACAATTGCTGTTGGACTAATGTG GGTAATGGGTGCTGCTGCTCTTCAAAAGTATATTGGTAGCTTAGGTGGAAT
genomic: CAAGAAATCTTCTCGACTGTGCTGTTTACAATTGCTGTTGGACTAATGTGgtatgttcaa ... tattttgcagGGTAATGGGTGCTGCTGCTCTTCAAAAGTATATTGGTAGCTTAGGTGGAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggattagttacttattgagataatttctttgttttggtgcttcatattttgcagGGTAATGGGTGCTGCTGCTCTTCAAAAGTATATTGGTAGCTTAGGTGGAATAGGGGCATCTGGTGTTGGTTCCAGTTCATCATATTCTCCTAAAGAATTG
ataatttctttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttgccgaaatatcattttcagtgcttcttgcatgggttttttttggattagttacttattgagataatttctttgttttggtgcttcatattttgcagGGTAATGGGTGCTGCTGCTCTTCAAAAGTATATTGGTAGCTTAGGTGGAATAGGGGCATCTGGTGTTGGTTCCAGTTCATCATATTCTCCTAAAGAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
-cttgccg
- - - - - - - - - - - gtgcttc
- - - - - - - - - - - -tgcttct
- - - - - - - - - - - - - - - tgcatgg