Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaataatgagaccaggctgcgcgcgcattcgctccatgcggctttccctgactcgcgccttcattcagGACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGAGAAGACGAGACCCACGTGTCGACCCGAGTCATGGGCACGCAGGGCTACG

Basic information

species Zea mays
transcript GRMZM2G110968_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110968_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S207_2V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------gtaaaataatgagaccaggctgcgcgcgcatt-cgctccatgcggctttccctgactcgcgccttcatt--------cagGACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGAGAAGACGAGACCCACGTGTCGACCCGAGTCATGGGCACGCAGGGCTACG
                    ||||  | || | |    | |      |||||   |  | |      | | ||| |    | |||  ||        ||||| ||||| || |||||||| ||||||||||||||||| | |||||||| || |||| | || ||||| || || || || ||||||||  | ||||| |
cagtaacgagttgcgtggaagtaacgttattataaagcgttattgttgcattatacctcttagtttgtcctctgtcctcagacttgtttatggttgtcagGATTACACAGCCAAGCTGTCTGATTTCGGGCTAGCGAAAGATGGACCTGAAGGAGACAAAACTCACGTTTCAACACGTGTTATGGGCACCTATGGCTATG

upper sequence: GRMZM2G110968_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ19239 (Selaginella moellendorffii), 3'ss of exon 4
gtaaaataatgagaccaggctgcgcgcgcattcgctccatgcggctttccc-tgactcgc-gccttcattcagGACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGAGAAGACGAGACCCACGTGTCGACCCGAGTCATGGGCACGCAGGGCTACG
|| |    | || |      ||      || ||           |   ||| |||||||     | |  ||||||||||||||| ||||| ||||||||||| || ||||| | ||| || | || |||| |||| || || || || ||| ||||||| ||  | |||||||
gtgagtagaagataaagaaatgaagaaacaatcttggagactaacaaacccgtgactcgttaaatcctctcagGACTACACGGCCAAGCTCTCGGATTTCGGCCTCGCGAAAGATGGCCCGGAAGGAGACAAGACGCATGTTTCCACACGAATCATGGGAACTTACGGCTACG

upper sequence: GRMZM2G110968_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ22709 (Selaginella moellendorffii), 3'ss of exon 4
gtaaaataatgagaccaggctgcgcgcgcattcgctccatgcggctttccc-tgactcgc-gccttcattcagGACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGAGAAGACGAGACCCACGTGTCGACCCGAGTCATGGGCACGCAGGGCTACG
|| |    | || |      ||      || ||           |   ||| |||||||     | |  ||||||||||||||| ||||| ||||||||||| || ||||| | ||| || | || |||| |||| || || || || ||| ||||||| ||  | |||||||
gtgagtagaagataaagtaatgaagaaacaatcttggagactaacaaacccgtgactcgttaaatcctctcagGACTACACGGCCAAGCTCTCGGATTTCGGCCTCGCGAAAGATGGCCCGGAAGGAGACAAGACGCATGTTTCCACACGAATCATGGGAACTTACGGCTACG

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|76020783|gb|DT947953.1|DT947953
EST:     AACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCG                         GACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGA
genomic: AACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCGgtaaaataat ... cttcattcagGACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGA
EST: gi|91049702|gb|EB160120.1|EB160120
EST:     AACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCG                         GACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGA
genomic: AACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCGgtaaaataat ... cttcattcagGACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGA
EST: gi|78089532|gb|DV517906.1|DV517906
EST:     AACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCG                         GACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGA
genomic: AACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCGgtaaaataat ... cttcattcagGACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGA
EST: gi|78089533|gb|DV517907.1|DV517907
EST:     AACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCG                         GACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGA
genomic: AACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCGgtaaaataat ... cttcattcagGACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGA
EST: gi|91054554|gb|EB164972.1|EB164972
EST:     AACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCG                         GACTACACGGGCGAA-CTGTCGGATTTCGGGCT
genomic: AACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCGgtaaaataat ... cttcattcagGACTACACGG-CGAAGCTGTCGGATTTCGGGCT
EST: gi|67019199|gb|CO447948.1|CO447948
EST:     AACCCGTCATCTACCGCGACTTCAAGACGTCCAACATTCTGCTGGACTCG                         GACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGA
genomic: AACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCGgtaaaataat ... cttcattcagGACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 2 RNA-Seq libraries.


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 21

GATCGCCATTGGAGCCGCCAAAGGTTTGGCTTTCCTCCACGACGCTGCCAAACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCGgtaaaataat ... cttcattcagGACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGAGAAGACGAGACCCACGTGTCGACCCGAGTCATGGGCACGCAGGGCTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 25

GATCGCCATTGGAGCCGCCAAAGGTTTGGCTTTCCTCCACGACGCTGCCAAACCCGTCATCTACCGCGACTTCAAGACGTCCAACATCCTGCTGGACTCGgtaaaataat ... cttcattcagGACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGAGAAGACGAGACCCACGTGTCGACCCGAGTCATGGGCACGCAGGGCTACG




<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggctgcgcgcgcattcgctccatgcggctttccctgactcgcgccttcattcagGACTACACGGCGAAGCTGTCGGATTTCGGGCTAGCGAAGGCTGGACCTGGAGAAGACGAGACCCACGTGTCGACCCGAGTCATGGGCACGCAGGGCTACG
                                ccctgac  putative branch site (score: 25)
                                            ccttcattc  putative PPT