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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgaaccctgtccagagctaatatgttttatccacttattattcacttatttggtgctgtatattaatttgaaactgatagtgaatatgtctgatcattgtctgttgattaaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG

Basic information

species Oryza sativa
transcript LOC_Os11g06760.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g06760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G050982_T01 (Zea mays), 3'ss of exon 5
---------------gtaagttgaaccctgtc-cagagctaatat-gttttatccacttattattcacttatttggt----gctgtatattaatttgaaactgatagtgaatatgtctgatcattgtctgttg------attaaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG
               ||    ||    | | | ||||   | |   |  ||   ||||| |  |||  | ||| |      | ||| || |  |||||||      || |   || ||| ||||| |  |||       |||   | ||||| ||||| ||||||||||||||||||||||||| ||| |||||||||||||| || ||||
gtaagtcaaaaacctgtcctctggctacggacacagaagaattgcagccttggtcacttttccttccttaattcgtaaatggttgtttactgttttgaaatcttctgtcagcttgcctgctcattattggttatgttctattttgtacttagATACCAACCACCTATCCCAGCTGAAGAAGTGAAACCTGCTTTTGACTATGACCATGAAG

upper sequence: LOC_Os11g06760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G146472_T02 (Zea mays), 3'ss of exon 6
gtaagttgaac-cctgtcca--------gagctaatatgttttatccacttattattcacttatttggtgctgtatattaatttgaaactgatagtg---aatatgtctgatcattgtctgtt------gattaaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG
||||||  ||  |||||||          | |  | | |  || | || ||  ||     ||  ||    ||   |  ||| |||    | |  ||    |   || ||| ||||| |  |||      |||    | ||||| |||||||||||||||||||||||||| |||| ||| |||||||||||||| || ||||
gtaagtcaaaaacctgtcctctcgctacaaacacagaagaattttacagttgatagctttttcctt--ccctaattcgtaaattgctgttcactgttttcagcttgcctgctcattattggttatgtttgatattgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGATCATGAAG

upper sequence: LOC_Os11g06760.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G146472_T03 (Zea mays), 3'ss of exon 5
gtaagttgaac-cctgtcca--------gagctaatatgttttatccacttattattcacttatttggtgctgtatattaatttgaaactgatagtg---aatatgtctgatcattgtctgtt------gattaaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG-----------------------------------------
||||||  ||  |||||||          | |  | | |  || | || ||  ||     ||  ||    ||   |  ||| |||    | |  ||    |   || ||| ||||| |  |||      |||    | ||||| |||||||||||||||||||||||||| |||| ||| |||||||||||||| || ||||                                         
gtaagtcaaaaacctgtcctctcgctacaaacacagaagaattttacagttgatagctttttcctt--ccctaattcgtaaattgctgttcactgttttcagcttgcctgctcattattggttatgtttgatattgtacttagATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGATCATGAAGGTGACATTCTCAGTTGATCTTCTCTTCCTAACGCTGTGGTC

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|38474629|gb|CF958762.1|CF958762
EST:     AGCACTGGATACGTTATCTCCAGG                         GTAGCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
genomic: AGCACTGGATACGTTATCTCCAGGgtaagttgaa ... aaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
EST: gi|218484821|gb|FG946766.1|FG946766
EST:     ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGG                         GTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
genomic: ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGGgtaagttgaa ... aaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
EST: gi|56157893|gb|C27653.2|C27653
EST:     ATGATCGCCATAACATTATCCAAGAA-GCACTTGATACGTTATCTCCAGG                         GTACCAGCCACCT
genomic: ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGGgtaagttgaa ... aaatccttagGTACCAGCCACCT
EST: gi|25799906|gb|CA755867.1|CA755867
EST:     ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGG                         GTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
genomic: ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGGgtaagttgaa ... aaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
EST: gi|66916064|gb|CX102912.1|CX102912
EST:     ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGG                         GTACCAGCCACCCATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
genomic: ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGGgtaagttgaa ... aaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
EST: gi|13818900|gb|AB060279.1|AB060279
EST:     ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGG                         GTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
genomic: ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGGgtaagttgaa ... aaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
EST: gi|29677609|gb|CB673884.1|CB673884
EST:     ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGG                         GTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
genomic: ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGGgtaagttgaa ... aaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
EST: gi|29677610|gb|CB673885.1|CB673885
EST:     ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGG                         GTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
genomic: ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGGgtaagttgaa ... aaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
EST: gi|86897912|gb|CI289086.1|CI289086
EST:     ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGG                         GTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
genomic: ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGGgtaagttgaa ... aaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA
EST: gi|38474027|gb|CF958159.1|CF958159
EST:     ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGN                         GTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATAA
genomic: ATGATCGCCATAACATTATCCAAGAAAGCACTGGATACGTTATCTCCAGGgtaagttgaa ... aaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgaaactgatagtgaatatgtctgatcattgtctgttgattaaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG
                                                tcctt  CT-rich tract
                                       ttgattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgaaccctgtccagagctaatatgttttatccacttattattcacttatttggtgctgtatattaatttgaaactgatagtgaatatgtctgatcattgtctgttgattaaatccttagGTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT