Sequence
atgc intronic sequence ATGC exonic sequence...catgttatttgtgatgacttctgcttataacatttatacttttttcctttgttgtacatgcacgtgacatatctaattatattctttatcttgtttacagGTTAGTGATTTGGAAAACCAAATCGATAACTTCGAAGCTGAGGTTGAAGGACTTTCAATTAAGAAAGGAAAGCAAAGACCTCCTCGATTG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g44900.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g44900.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G340749_T01 (Zea mays), 3'ss of exon 2
catgttatttgtgatgacttctgcttataacatttatacttttttcctttgtt-gtacatgca---cgtgacatatctaattatattctttatcttgtttacagGTTAGTGATTTGGAAAACCAAATCGATAACTTCGAAGCTGAGGTTGAAGGACTTTCAATTAAGAAAGGAAAGCAAAGACCTCCTCGATTG
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--tgtggttacagatggctcttgct-atgactattatttgctttattgttgtaagtgcttgcaatatctaatgtacctt-ttggaccatgttatttttttacagGTTAGTGATTTGGAAAGCCAGATTGATAACTTCGAAGCAGAGATTGAAGGACTTTCAATTAAAAAGGGAAAACAAAGACCGCCTCGATTG
upper sequence: LOC_Os03g44900.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 5
catgttatttgtgatgacttc-tgcttataacatttatacttttttcctttgttgtacatgcacgtgacatatctaattatattctt------tatcttgtttacagGTTAGTGATTTGGAAAACCAAATCGATAACTTCGAAGCTGAGGTTGAAGGACTTTCAATTAAGAAAGGAAAGCAAAGACCTCCTCGATTG
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-------cccatgaggccttgacacctactatggctattattagctttattgttgcaagtgcttgcgatatctctaatatacttcttggaccatgtatttcttacagGTTAGCGATTTGGAAAGCCAGATTGATAACTTCGAAGCAGAGATTGAAGGGCTTTCAATTAAAAAGGGAAAGCAAAGACCGCCTCGATTG
upper sequence: LOC_Os03g44900.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 4
catgttatttgtgatgactt-ctgcttataacat-ttatacttttttcctttgttgtacatgcacgtgacatatctaattatattctttatct---tgttta--cagGTTAGTGATTTGGAAAACCAAATCGATAACTTCGAAGCTGAGGTTGAAGGACTTTCAATTAAGAAAGGAAAGCAAAGACCTCCTCGATTG
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-------tctgtattcatgtgttatttagaagaggttatatttagttcgaatagtgtacttatatttctttctctggaaaacattattgttttaaatgtttgagtagGTTGGGGAGTTAGAAAATCAGATTGATAACTTTGAAGCTGAGCTTGAAGGACTTTCTGTCAAGAAAGGAAAGAACAGGCCTCCCAGATTG
upper sequence: LOC_Os03g44900.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G07830.1 (Glycine max), 3'ss of exon 4
catgttatttgtgatgactt-ctgcttataaca-tttatacttttttcctttgttgtacatgcacgtgacatatctaa-----ttatattctttatcttgtttacagGTTAGTGATTTGGAAAACCAAATCGATAACTTCGAAGCTGAGGTTGAAGGACTTTCAATTAAGAAAGGAAAGCAAAGACCTCCTCGATTG
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-------tctgtattcatgtgttatttataagagcttatatttagttcaaatagtgtacttatatttctttctctggaaaatgttataattttaaatgtttgagtagGTTGGGGAGTTAGAAAATCAAATCGATAACTTTGAAGCTGAGCTTGAGGGACTTTCTGTCAAGAAAGGAAAGAACAGGCCACCCAGATTGMapped 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|66918088|gb|CX104936.1|CX104936EST: AAAGCTGAAACAAGAGATTGG-TTAACAATGTG GTTAGTGATTTGGAAAACCAAATCGATAACTTCGAAGCTGAGGTTGAAGGA
genomic: AAAGCTGAAACAAGAGATTGGCTTAACAATGTGgtatgttaga ... ttgtttacagGTTAGTGATTTGGAAAACCAAATCGATAACTTCGAAGCTGAGGTTGAAGGA
EST:
gi|29630458|gb|CB635467.1|CB635467EST: ATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG GTTAGTGATTTGGAAAACCAAATCGATAACTTCGAAGCTGAGGTTGAAGGA
genomic: ATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTGgtatgttaga ... ttgtttacagGTTAGTGATTTGGAAAACCAAATCGATAACTTCGAAGCTGAGGTTGAAGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttgttgtacatgcacgtgacatatctaattatattctttatcttgtttacagGTTAGTGATTTGGAAAACCAAATCGATAACTTCGAAGCTGAGGTTGAAGGACTTTCAATTAAGAAAGGAAAGCAAAGACCTCCTCGATTG
atctaat putative branch site (score: 3)
ttctttatcttgttt putative PPT
atatctaattatattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgttatttgtgatgacttctgcttataacatttatacttttttcctttgttgtacatgcacgtgacatatctaattatattctttatcttgtttacagGTTAGTGATTTGGAAAACCAAATCGATAACTTCGAAGCTGAGGTTGAAGGACTTTCAATTAAGAAAGGAAAGCAAAGACCTCCTCGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
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