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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtctctgtccttgactttatgttgtttaataattttgcagatatgtcttcacattccatatcttacccttttcattgcatttcacactcgttcattttgttcctgttcttctaacatcatatctgtaatcacgttttatcctttcagtgcattcatacttctacgctgtgtttctcttcagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAAGAGGAGCAT

Basic information

species Oryza sativa
transcript LOC_Os02g45480.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g45480.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G037200_T02 (Zea mays), 3'ss of exon 6
gttagtctctgtccttgactttatgttgtttaataattttgcagatatgtcttcacattccatatcttacccttttcattgcatttcacactcgttcattttgttcc-tgttcttctaacatcatatctgtaatcacgttttatcctttcagtgc-attcatacttctacgctgtgtttctcttcagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAAGAGGAGCAT
                                                                          ||  | ||  |  |||     ||||||||||   |  | |  |||     | ||  || |     |||  | | |||  ||  |||||  |||||     | |||     ||||||||||| |||||||| ||||||| ||| |||||||||||||||||||||||||| || 
-------------------------------------------------------------------------gttagtcgccatctacatc--atcattttgttgagtaatttcataattctctgtcgatattaggtatttcccttgtcaaagctgttcatggttctaataattattttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG

upper sequence: LOC_Os02g45480.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G037200_T01 (Zea mays), 3'ss of exon 6
gttagtctctgtccttgactttatgttgtttaataattttgcagatatgtcttcacattccatatcttacccttttcattgcatttcacactcgttcattttgttcctgttcttctaacatcatatctgtaatcacgttttatcctttcagtgc-attcatacttctacgctgtgtttctcttcagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAAGAGGAGCAT
                                                                                                           |  | |  |||     | ||  || |     |||  | | |||  ||  |||||  |||||     | |||     ||||||||||| |||||||| ||||||| ||| |||||||||||||||||||||||||| || 
----------------------------------------------------------------------------------------------------------gtaatttcataattctctgtcgatattaggtatttcccttgtcaaagctgttcatggttctaataattattttggcgcagGTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG

upper sequence: LOC_Os02g45480.4 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv16s0100g00320.t01 (Vitis vinifera), 3'ss of exon 7
gttagtctctgtccttgactttatgttgtttaataattttgcagatatgtcttcacattccatatcttacccttttcattgcatttcacactcgttcattttgttcctgttcttctaacatcatatctgtaatcacgttttatcctttcagtgcattcatacttctacgctgtgtttctctt-cagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAAGAGGAGCAT
                                                              | ||||    || |   ||||||| |  ||  |  ||||||  |    |  | | |  |  ||    |  | | ||||| |||  ||  |    |  |         || ||||||| |  ||||||||||  || |||||||||||||  |||||||||||||| || ||||| || || || 
-----------------------------------------------------------gtttgtcttctttttattcatgcattt-atccttata-attttgcactgaatgctatcaagttctaagcattctaa-gttttctcccctctctctggttttttcctcttactttgtttctttggcagGTTTGGGTTGCAACAGAAAGTGGAAATTTGGAAGTAACATACACCCACAATGAAGAACAG

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|29675454|gb|CB671729.1|CB671729
EST:     TGTGTTGGGATCAATTCCTATTATCATGTTCCTTGGATCAAACAATAAAA                         GTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAA
genomic: TGTGTTGGGATCAATTCCTATTATCATGTTCCTTGGATCAAACAATAAAAgttagtctct ... ttctcttcagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAA
EST: gi|218479278|gb|FG957154.1|FG957154
EST:     TGTGTTGGGATCAATTCCTATTATCATGTTCCTTGGATCAAACAATAAAA                         GTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAA
genomic: TGTGTTGGGATCAATTCCTATTATCATGTTCCTTGGATCAAACAATAAAAgttagtctct ... ttctcttcagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAA
EST: gi|29618177|gb|CB623189.1|CB623189
EST:     TGTGTTGGGATCAATTCCTATTATCATGTTCCTTGGATCAAACAATAAAA                         GTTTGTGCAGTTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAA
genomic: TGTGTTGGGATCAATTCCTATTATCATGTTCCTTGGATCAAACAATAAAAgttagtctct ... ttctcttcagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAA
EST: gi|29657539|gb|CB653814.1|CB653814
EST:     TGTGTTGGGATCAATTCCTATTATCATGTTCCTTGGATCAAACAATAAAA                         GTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAA
genomic: TGTGTTGGGATCAATTCCTATTATCATGTTCCTTGGATCAAACAATAAAAgttagtctct ... ttctcttcagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAA
EST: gi|33794977|gb|CF323368.1|CF323368
EST:     TGTGTTGGGATCAATTCCTATTATCATGTTCCTTGGATCAAACAATAAAA                         GTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAA
genomic: TGTGTTGGGATCAATTCCTATTATCATGTTCCTTGGATCAAACAATAAAAgttagtctct ... ttctcttcagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAA
EST: gi|58674413|gb|CK063099.1|CK063099
EST:     TGTGTTGGGATCAATTCCTATTATCATGTTCCTTGGATCAAACAATAAAA                         GTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAA
genomic: TGTGTTGGGATCAATTCCTATTATCATGTTCCTTGGATCAAACAATAAAAgttagtctct ... ttctcttcagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcacgttttatcctttcagtgcattcatacttctacgctgtgtttctcttcagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAAGAGGAGCAT
                                       ctgtgtttctcttc  CT-rich tract
       ttttat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtctctgtccttgactttatgttgtttaataattttgcagatatgtcttcacattccatatcttacccttttcattgcatttcacactcgttcattttgttcctgttcttctaacatcatatctgtaatcacgttttatcctttcagtgcattcatacttctacgctgtgtttctcttcagGTTTGGGCAGCTACAGAAAGTGGAAGCTTGGAAGTAACATATACACACAAAGAGGAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA