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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTAGCACAAACTTGGAAGCGATTCAAATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttcttccaaaagctgtactatcggaaatatttcaacatttgatgtccttcaatagattagtttctaatcagtcattagtgtgatagtttgtgcca...

Basic information

species Oryza sativa
transcript LOC_Os03g42220.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42220.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G058276_T01 (Zea mays), 5'ss of exon 7
GGTAGCACAAACTTGGAAGCGATTCAAATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttcttccaaaagctgtactatcggaaatatttcaacatttgatgtccttcaatagattagtt-tctaatcagtcattagtgtgatagtttgtgcca
|||||||| ||||||||| | |||||||||||||||| |||||||||||| |||||||| || |||||||| |||||||||||  ||  | ||    | | |   ||    ||| | ||            |   |    | || ||| | |   ||  |   |  |  ||| || ||
GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTCAAGGATTCATTTTTGGACGAAGGgtatgtatttatagaaaaattgccacttgattcttttgaccacacagcactgggctgcatgcaaattctctcacctagcaccaa-attctcctttctgtca

upper sequence: LOC_Os03g42220.2 (Oryza sativa), 5'ss of exon 7
lower sequence: EF517601.1_FGT012 (Zea mays), 5'ss of exon 16
GGTAGCACAAACTTGGAAGCGATTCAAATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttcttccaaaagctgtactatcggaaatatttcaacatttgatgtccttcaatagattagtt-tctaatcagtcattagtgtgatagtttgtgcca
|||||||| ||||||||| | |||||||||||||||| |||||||||||| || ||||| ||||||||||| |||||||||||  ||    ||    | | |   ||    ||| | |             |   |    | || ||| | |   ||  |   |  |  |||  | | 
GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtatttatgtaaaaaatgccaattgattcttttgaccgcacagcactaggctgcatgcaaattctctcacctagcaccaagttctttctttccgtc-

upper sequence: LOC_Os03g42220.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT5G20890.1 (Arabidopsis thaliana), 5'ss of exon 8
GGTAGCACAAACTTGGAAGCGATTCAAATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttcttccaaaagctgtactatcggaaatatttcaacatttgatgtcctt--caatagattagtttctaatcagtcattagt--gtgatagtttgtgcca---
|| ||||||||||||||||| ||||| ||  | || | ||||||||| || || ||||| || ||||||||||||||||| |     | | |   ||| |  | ||    | ||||| |||   | | ||   | || |||   | | || | | ||||  ||   || ||  |  || |    
GGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGGgtaaga----caacactttgtgcctttggcgtcagttcaa-attcagttttctgagctattgatctttctttagt-attcatctgttcatggtaactc-tgtcgtgt

upper sequence: LOC_Os03g42220.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 5'ss of exon 9
GGTAGCACAAACTTGGAAGCGATTCAAATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttcttccaaaagctgtactatcggaaatatttcaacatttg-atgtccttcaatagattagtttctaatcagtcattagtgtgatagtttgtgcca
|| ||||||||||||||  | ||||||||| | ||||  ||||||||||| ||||| ||||| ||||||||||||||||| |  | |  |||   || |||        ||||      |||  ||||    ||  |||        | ||||||| ||     ||     |   | |
GGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGGgta-gagcatataaactatgaacttcatattgtattattcagtttacatgtttaacagaagaacgaagcatcatcagtcgttttgtagactaagtacacaa

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|58685627|gb|CK074314.1|CK074314
EST:     ATTCTGAAGAAACCTGGAGGATCCCTCAAGGACTCCTTTTGGGATGAAGG                         TTTCATTCTTGACAAGAAAATCGGTCTTGGACAACCAAAGAGAATTGAGAA
genomic: ATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttctt ... tgttttgcagTTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAA
EST: gi|66918817|gb|CX105665.1|CX105665
EST:     ATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTNGGATGAAGG                         TTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAA
genomic: ATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttctt ... tgttttgcagTTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAA
EST: gi|58656007|gb|CK044687.1|CK044687
EST:     GGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGG                         TTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAA
genomic: GGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttctt ... tgttttgcagTTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAA
EST: gi|29676853|gb|CB673128.1|CB673128
EST:     ATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGG                         TTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGA
genomic: ATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttctt ... tgttttgcagTTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGA
EST: gi|58686292|gb|CK074979.1|CK074979
EST:     ATTCTGAAGAAACCTGGAGGATCCCTCAAGGACTCCTTTTAGGATGAAGG                         TTTCATTCTTGACAAGAAAA-TGGTCTTGGACAACCAAAGAGAATTGAGAA
genomic: ATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttctt ... tgttttgcagTTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAA
EST: gi|29616345|gb|CB621357.1|CB621357
EST:     ATTCTGAAGAAACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGG                         TTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCANAGAGAATTGAGAA
genomic: ATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttctt ... tgttttgcagTTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAA
EST: gi|218488070|gb|FG946099.1|FG946099
EST:     ATTCTGAAGAAACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGG                         TTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAA
genomic: ATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttctt ... tgttttgcagTTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAA
EST: gi|58681953|gb|CK070640.1|CK070640
EST:     ATTCTGAAGAAACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGG                         TTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAA
genomic: ATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttctt ... tgttttgcagTTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTAGCACAAACTTGGAAGCGATTCAAATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttcttccaaaagctgtactatcggaaatatttcaacatttgatgtccttcaatagattagtttctaatcagtcattagtgtgatagtttgtgcca

- - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - -  GAGGAT