Sequence
atgc intronic sequence ATGC exonic sequence...tcttctttacgcagatctcagtgttctgtgactttttttttatgaaagttaaatataatcataaccctattttagtcattaaatttttttttctgaacagGTGACCATTATGTTTGTGACCCTCGAGAAAATTGCTCAAGTGGAACCTAAATATGTTGACATTGTACTATTGGAGAATTATGCAGCTTTCCAGCACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g17600.3 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g17600.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G060949_T01 (Zea mays), 3'ss of exon 7
---------------------------------------------------------tcttctttacgcagatctcagtgttctgtgactttttttttatgaaagttaaat--ataatcataaccctattttagtcattaaatttttttttctgaacagGTGACCATTATGTTTGTGACCCTCGAGAAAATTGCTCAAGTGGAACCTAAATATGTTGACATTGTACTATTGGAGAATTATGCAGCTTTCCAGCACAG
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gtatgaacttactataacattcaccattcaatgctaaacaccatttaacaaaatatacgccaactactgatgcatttgcaaccgatgttggccatttcataccactccgatttgtatttgcgcctctaattaacttaccatatgtgactg---aaatagGTTACCATTATGTTTGTCATTCTGGAGAAAATTGCTCAAGTGGAACCTAAATATGTTGATATTGTACTTTTGGAAAACTATGCAGCTTTCCAGCACAG
upper sequence: LOC_Os11g17600.1 (Oryza sativa), 3'ss of exon 19
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 19
tcttctttacgcagatctcagtgt-tctgtgactttttttttatgaaagttaaatataatcataaccctattttagtcattaaatttttttttctga------acagGTGACCATTATGTTTGTGACCCTCGAGAAAATTGCTCAAGTGGAACCTAAATATGTTGACATTGTACTATTGGAGAATTATGCAGCTTTCCAGCACAG
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----agtaaagtatatctcagattgtctctgcatttactatcgtcaatttc---ttttgtttctttccttgtttagctgatagagtctgactcctaatgttttatagGTGAGCATACTGTTTGTGACCCTCGAGAAAATTGCCCAACAAGATCCTAAATATGCAGATATTCTCCTTTTGGAAAACTATGCTGCTTTTCAAACTTG
upper sequence: LOC_Os11g17600.1 (Oryza sativa), 3'ss of exon 19
lower sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 19
tcttctttacgcagatctcagtgttctgtgactttttttttatgaaagttaaatataatcataaccctattttagtcattaaatttttttttctga------acagGTGACCATTATGTTTGTGACCCTCGAGAAAATTGCTCAAGTGGAACCTAAATATGTTGACATTGTACTATTGGAGAATTATGCAGCTTTCCAGCACAG
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---agttcacttacaaataaatagaa-atgaagtatatctca-gattgtttcttttctttctc-tcctgctttggttgacagagtctgactactgctattttatagGTGAGCATAATGTTTGTGACCCTCGAGAAAATTGCCCAACAAGATCCTAAATATGCAGATATTCTCCTGTTAGAAAACTATGCTGCTTTTCAGAATAG
upper sequence: LOC_Os11g17600.1 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 19
tcttctttacgcagatct--cagtgttctgtgactttttttttatgaaagttaaatataatcata-accctattttagtcattaaatttttttttctgaacagGTGACCATTATGTTTGTGACCCTCGAGAAAATTGCTCAAGTGGAACCTAAATATGTTGACATTGTACTATTGGAGAATTATGCAGCTTTCCAGCACAG
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--ccatctattaagttttagtagtggtttaagagattgtagcaatgcttgttatttattataagagattcaattccatgaagtgggacctattgtttga-cagGTTACCATAATGTTTGTGACTTTGGAGAAAATTGCACAAACCGACCCAAAATATGCTGATATTTTGCTTTTGGAGAATTTTGCAGCTTTCCAGAATAGMapped 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|87020968|gb|CI269685.1|CI269685EST: ATCCAGGGATCTAGTTGATCAGGCCTATACGAAAATT GTGACCATTATGTTTGTGACCCTCGAGAAAATTGCTCAAGTGGAACCTAAA
genomic: ATCCAGGGATCTAGTTGATCAGGCCTATACAAAAATTgtaagacttt ... ttctgaacagGTGACCATTATGTTTGTGACCCTCGAGAAAATTGCTCAAGTGGAACCTAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttaaatataatcataaccctattttagtcattaaatttttttttctgaacagGTGACCATTATGTTTGTGACCCTCGAGAAAATTGCTCAAGTGGAACCTAAATATGTTGACATTGTACTATTGGAGAATTATGCAGCTTTCCAGCACAG
tcataac putative branch site (score: 2)
tttttttttct putative PPT
tattttagtcattaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttctttacgcagatctcagtgttctgtgactttttttttatgaaagttaaatataatcataaccctattttagtcattaaatttttttttctgaacagGTGACCATTATGTTTGTGACCCTCGAGAAAATTGCTCAAGTGGAACCTAAATATGTTGACATTGTACTATTGGAGAATTATGCAGCTTTCCAGCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - -tgttctg