Sequence
atgc intronic sequence ATGC exonic sequencegtaaatgcggttgtttgcacctatgtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g44922.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G004932_T01 (Zea mays), 3'ss of exon 6
gtaaatgcggttgtttgcacctatgtgata--tagctcttctgattggtca--ttgtctcatgtgcttatgtacattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTCAAG
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gtaaacatgattgcacctattgatataacacataactcttctgattggagaagttgactgatatactagagcgccttatccagGTGTATATCATTGGAGGAGATGGAACTCAGAAGGGAGCATATGAGATCTTCAAG
upper sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 6
--------------gtaaatgcggttgtttgcacctatgtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTCAAG
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gtctgcattgcattctatttattacaacatataacttcattttgtatgtagtaacatcagtagtctaataaattactcaatcaattccaccagGTTTATATAATTGGAGGAGATGGAACTCAGAGGGGTGCAGATAGGATTTTTGAG
upper sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------gtaaat--gcggttgtttgcacctatgtgat-atagctcttctgattggtcattgtctcatgtgcttatgtacatta---------cccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTCAAG
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gtttaccatgtgtcagctgtattataatgaagtttctgatgatgatgaatgcgggaatcataaattagagttttgttatatccatgtacttaaaacctaagtaggttattgtcatcgcatgggttttcattgcttgggttatggttacagGTTTATATTATTGGAGGAGATGGAACACAGAGAGGAGCGACTGTGATTTACGAG
upper sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 6
--------------------------------------------------------gtaaatgcgg---ttgtttgcacctatgtgat-atagctcttctgattggtcattgtctcatgtgctt-----atgtacattacc----cagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTCAAG
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gtttaccatgtgtcaactgtattataatgaagtttctaatgatgatgaatgcaatcataaatttagagttttgttatatccatgtacttaaaacctaagtaggttattgtcatcgcatgggttttcattgtttgggttatggttacagGTTTATATTATTGGAGGAGATGGAACACAGAGAGGAGCGACTGTGATTTACGAG
upper sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 6
gtaaatgcggttgtttgcacctatgtg-atatagctct-tctgattggtcattgtctcatgtgcttatgtacatta--cccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTCAAG
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--gtctgcacttctttcaatgtagcagtatatatttttgtgtgccgtgtaagtacatcagattaatatctctctgaatttcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTTGAG
upper sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 6
gtaaatgcggttgtttgcacctatgtg-atatagctcttctgattggtcattgtctcatgtgcttatgtacattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTCAAG
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------------gtctgcatttctttctatttagcagtagtgtatgtacatcagatta-acatctctctgaatt--tcagGTTTATATAATTGGAGGAGATGGAACTCAGAAGGGTGCATCTGCAATTTTTGAG
upper sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------gtaaatgcggttgtttg-cacctatgtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTCAAG
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tgaagatcgcttcaaaacttttcgatgccggcctcagtcacctcatcaacctcgtattttttgcaatacagctcaccctgtgacattgatttgacttcagGTCTATATCATTGGAGGAGATGGCACTCAGAAAGGAGCTAATGCTATCCACGAGMapped 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|569752|gb|D40601.1|D40601EST: ATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAG GTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTC
genomic: ATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcgg ... cattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTC
EST:
gi|571842|gb|D41353.1|D41353EST: ATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAG GTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATTGAGATCTT
genomic: ATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcgg ... cattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATAT-GAGATCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTCAAG
ttctgat putative branch site (score: 3)
ttatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatgcggttgtttgcacctatgtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC