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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacctctcccatttctgaaacaaatttctttttgttttgtgctgtattttgttgtttttccataccagtaacgtttctgcctcttatatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCAATTGAGGAGGTGCGTGTAACGCGTGATAAAGGTTTTGGCTTTGTGCGTT

Basic information

species Oryza sativa
transcript LOC_Os11g40510.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 10
-----------------------------gtaacctctcccatttctgaaacaaa-tttctttttgttttgtgctgtattttgttgtttttccataccagtaacgtttctgcctcttatatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCAATTGAGGAGGTGCGTGTAACGCGTGATAAAGGTTTTGGCTTTGTGCGTT
                                |  | | |  |   ||        ||||| |||| | |   || | |||||||   ||||  |   | |  |   | || ||  | | |||   |||  | ||  ||||||||||||   |||||||||||||| |||| ||||||||||||||| || |||||||| ||||||||||| |||||||||||| | |
gtattactcttccaatagaacagctgctgtctatgtttactgtgcttgtgtttggctttctatttgctcttaccttttttttgttagctttct-ttttattgtctaatttgtcttattt-tttttcagGCTACCATGAATGATGTGCACCTGTTTTTCCATTCACTGGGGGCTGGTTCAATTGAGGAAGTCCGTGTAACTCGTGATAAAGGCTTTGGCTTTGTGAGGT
















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|218488516|gb|FG953157.1|FG953157
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|29641559|gb|CB646566.1|CB646566
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|218492528|gb|FG964892.1|FG964892
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|88690783|gb|CI734862.1|CI734862
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|218488001|gb|FG950016.1|FG950016
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGNT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|88689298|gb|CI732874.1|CI732874
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|58688359|gb|CK077046.1|CK077046
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATG
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATG
EST: gi|58687280|gb|CK075967.1|CK075967
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTT
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTT
EST: gi|29640531|gb|CB645540.1|CB645540
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|58602505|gb|CK013033.1|CK013033
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCCACAGCAATGATGTGCACAGATTTTTCCAT
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCAT
EST: gi|87019113|gb|CI297314.1|CI297314
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|33680119|gb|CF308358.1|CF308358
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGGTTGGTTC
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGG-TTGGTTC
EST: gi|218498744|gb|FG958423.1|FG958423
EST:     GGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: GGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|88691922|gb|CI735497.1|CI735497
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|88572117|gb|CI663688.1|CI663688
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGAT
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGAT
EST: gi|58587445|gb|CF985753.1|CF985753
EST:     CTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: CTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|218482201|gb|FG960522.1|FG960522
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|218500911|gb|FG960833.1|FG960833
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|58597389|gb|CK007917.1|CK007917
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|58606512|gb|CK034545.1|CK034545
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCCACAGCCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTC
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGC-AATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTC
EST: gi|86596642|gb|CI286555.1|CI286555
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTC
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTC
EST: gi|87004665|gb|CI300987.1|CI300987
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGG
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtattttgttgtttttccataccagtaacgtttctgcctcttatatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCAATTGAGGAGGTGCGTGTAACGCGTGATAAAGGTTTTGGCTTTGTGCGTT
                        cagtaac  putative branch site (score: 2)
                                tttctgcctcttat  CT-rich tract
                                        tcttatatttacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacctctcccatttctgaaacaaatttctttttgttttgtgctgtattttgttgtttttccataccagtaacgtttctgcctcttatatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCAATTGAGGAGGTGCGTGTAACGCGTGATAAAGGTTTTGGCTTTGTGCGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG