Sequence
atgc intronic sequence ATGC exonic sequence...cgttcgttggtggatttggatgccttcgagatgcgcacgtcacatcattgacttgtgattttttttcttcttcttttttgcgtgcttggttggtctgcagTTGGATACGGTTCCTACTTCGGCAAGAAGCTGGACCCGGAGCCCGGACGGTGCCGGCGTACGGACGGCAAGAAGTGGCGGTGCTCCAAGGAGGCCGCGCC
Basic information
species | Oryza sativa |
transcript | LOC_Os04g51190.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g51190.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G129147_T01 (Zea mays), 3'ss of exon 2
---cgttcgttggtggatttggatgccttcgagatgcgcacgtcacatcattgacttgtgattttttttcttcttcttttttgcgtgcttggttggtctgcagTTGGATACGGTTCCTACTTCGGCAAGAAGCTGGACCCGGAGCCCGGACGGTGCCGGCGTACGGACGGCAAGAAGTGGCGGTGCTCCAAGGAGGCCGCGCC
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gttcgtacgcacgtacacgtgtat-cttgccagccgtagccattg-actctcactctctcactggggttca-ctcctcttgcgtgtgtgtggtttccttgcagTTGGGTACGGGCCCTACTTCGGCAAGAAGGTGGACCCGGAGCCCGGGCGGTGCCGGCGTACGGACGGCAAGAAGTGGCGGTGCTCCAAGGAGGCCGCCCC
upper sequence: LOC_Os04g51190.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G041223_T01 (Zea mays), 3'ss of exon 2
cgttcgttggtggatttgg-atgc-cttcgagatgcgcacgtcacatcattgacttgt--gattttttttcttcttcttttttgcgtgcttggttggtctgcagTTGGATACGGTTCCTACTTCGGCAAGAAGCTGGACCCGGAGCCCGGACGGTGCCGGCGTACGGACGGCAAGAAGTGGCGGTGCTCCAAGGAGGCCGCGCC
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---acgcacgtacacatggtatgcgcaccgtgctgctggccata-gccgttgactcaccgggattcactcctctctcgcgtgtgtgtgtgtggcttccttgcagTTGGGTACGGGCCCTACTTCGGCAAGAAGGTGGACCCGGAGCCCGGGCGGTGCCGGCGTACGGACGGCAAGAAGTGGCGGTGCTCCAAGGAGGCCGCCCC
upper sequence: LOC_Os04g51190.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ24024 (Selaginella moellendorffii), 3'ss of exon 2
----------------------cgttcgttggtggatttggatgccttcgagatgcgcacgtcacatcattgacttgtgattttttttcttcttcttttttgcgtgcttggttggtctgcagTTGGATACGGTTCCTACTTCGGCAAGAAGCTGGACCCGGAGCCCGGACGGTGCCGGCGTACGGACGGCAAGAAGTGGCGGTGCTCCAAGGAGGCCGCGCC
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gtgagtgcctgctgcctttctcccttcacttcactgctcgactgcctcctcgctgttctcagcaccttgcaccactggcaactctaaagatctccttgctttcctgtgcagTGGG-CTGGGGAAACTTCCACCTTGGAATTCCG-AACAATCCCGACCCGGAGCCTGGTCGGTGCCGACGAACAGACGGCAAGAAGTGGAGGTGCTCCAGGGA---------
upper sequence: LOC_Os04g51190.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ24588 (Selaginella moellendorffii), 3'ss of exon 2
----------------------cgttcgttggtggatttggatgccttcgagatgcgcacgtcacatcattgacttgtgattttttttcttcttcttttttgcgtgcttggttggtctgcagTTGGATACGGTTCCTACTTCGGCAAGAAGCTGGACCCGGAGCCCGGACGGTGCCGGCGTACGGACGGCAAGAAGTGGCGGTGCTCCAAGGAGGCCGCGCC
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gtgagtgcctgctgcctttctcccttcacttcactgctcgactgcctcctcgccgttctcagcaccttgcaccactggcaactctaaagatctccttgctttcctgtgcagTGGG-CTGGGGAAACTTTCACCTTGGAATTCCG-AACAATCCCGACCCGGAGCCTGGTCGGTGCCGACGAACAGACGGCAAGAAGTGGAGGTGCTCCAGGGA---------Mapped 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|58659028|gb|CK047708.1|CK047708EST: CCGCCGTGGCCTCGACTCACTCGCCTCGCGCTTCTACCACCACCCTGTCC TTGGATACGGTTCCTACTTCGGCAAGAAGCTGGACCCGGAGCCCGGACGGT
genomic: CCGCCGTGGCCTCGACTCACTCGCCTCGCGCTTCTACCACCACCCTGTCCgtacgtgccc ... tggtctgcagTTGGATACGGTTCCTACTTCGGCAAGAAGCTGGACCCGGAGCCCGGACGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattgacttgtgattttttttcttcttcttttttgcgtgcttggttggtctgcagTTGGATACGGTTCCTACTTCGGCAAGAAGCTGGACCCGGAGCCCGGACGGTGCCGGCGTACGGACGGCAAGAAGTGGCGGTGCTCCAAGGAGGCCGCGCC
cattgac putative branch site (score: 3)
attttttttcttcttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgttcgttggtggatttggatgccttcgagatgcgcacgtcacatcattgacttgtgattttttttcttcttcttttttgcgtgcttggttggtctgcagTTGGATACGGTTCCTACTTCGGCAAGAAGCTGGACCCGGAGCCCGGACGGTGCCGGCGTACGGACGGCAAGAAGTGGCGGTGCTCCAAGGAGGCCGCGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - -gttggtg
- - - - - - - - tggatgc
- - - - - - - - - - - - - - - -tgcgcac
- - - - - - - - - - - - - - - - - - - - - - - - tgacttg