ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TACTACTATTTCTGTTTTACTCGAAGACATACCAGGGGGGAGGTTGGGTCCGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAGgtaaaattactcagtcagaagttgcattttaatgccagttttctttctaaatataacttctattgtaatcaacatacag

Basic information

species	Zea mays
transcript	GRMZM2G098815_T04
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G098815_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g09610.1 (Oryza sativa), 5'ss of exon 6

TACTACTATTTCTGTTTTACTCGAAGACATACCAGGGGGGAGGTTGGGTCCGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAGgtaaaa-------ttactcagtcagaagttgcattttaatgccagttttctttctaaatataacttctattgtaatcaacatacag
|  | || || ||| ||||||| |||| | | || |||| || ||||||||||||||||| || |||||||||||||||||||   || ||||||| ||||||| |       |||  ||| ||  |||||||| |   | || ||| | ||||||| |  ||||    |||||   |||||||||
TTTTGCTCTTGCTGGTTTACTCCAAGAAAAATCATGGGGAAGATTGGGTCCGCAATGGATACGACCCACACCCCCAAGACTTCACATACTTGATGGAGAGgtaacagagtgtcttagccagccaagagttgcatctgtgtacccgttctgtttctaagtgcaactgtgcttgtatcgaacatacag

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|71438169|gb|DR819219.1|DR819219

EST:     CGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAG                         CTACAATGGCTGAACCCTGANCA-TAACCACGAGCTATTATGGGATTATAG
genomic: CGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAGgtaaaattac ... caacatacagCTACAATGGCTGAACCCTGA-CAATAACCACGAGCTATTATGGGATTATAG

EST: gi|148952745|gb|EC898726.2|EC898726

EST:     CGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAG                         CTACAATGGCTGAACCCTG
genomic: CGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAGgtaaaattac ... caacatacagCTACAATGGCTGAACCCTG

EST: gi|71438316|gb|DR819366.1|DR819366

EST:     CGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAG                         CTACAATGGCTGA
genomic: CGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAGgtaaaattac ... caacatacagCTACAATGGCTGA

EST: gi|74245464|gb|DT653378.1|DT653378

EST:     CGCA-TGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAG                         CTACAATGGCTGAACCCTGACAATAACCACGAGCTATTATGGGATTATAGC
genomic: -GCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAGgtaaaattac ... caacatacagCTACAATGGCTGAACCCTGACAATAACCACGAGCTATTATGGGATTATAGC

EST: gi|71433709|gb|DR814759.1|DR814759

EST:     CGCAATGGATTCGGCCCACACCCTCAAGACTTCTTTTATTTGATGGGGAG                         CTACAATGGCTGAACCCTGACAATAAACACGAGCTATTATGGGATTATAGC
genomic: CGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAGgtaaaattac ... caacatacagCTACAATGGCTGAACCCTGACAATAACCACGAGCTATTATGGGATTATAGC

EST: gi|76926415|gb|DV170849.1|DV170849

EST:     CGCAATGGATTCGGCCCAC-CCCCCAAGACTTCCTTTATTTGATGGGGAG                         CTACAATGGCTGAACCCTGA
genomic: CGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAGgtaaaattac ... caacatacagCTACAATGGCTGAACCCTGA

EST: gi|71765717|gb|DR963654.1|DR963654

EST:     CGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAG                         CTACAATGGCTGAACCCTGACAATAACCACGAGCTATTATGGGATTATAGC
genomic: CGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAGgtaaaattac ... caacatacagCTACAATGGCTGAACCCTGACAATAACCACGAGCTATTATGGGATTATAGC

EST: gi|91873215|gb|EB403172.1|EB403172

EST:     GCAATGGATTCGGCCCACACCCCTCA-GACTTCCTTTATTTGATGGGGAG                         CTACAATGGCTGAACCCTGACCATATC-ACGAGCTAT
genomic: GCAATGGATTCGGCCCACACCCC-CAAGACTTCCTTTATTTGATGGGGAGgtaaaattac ... caacatacagCTACAATGGCTGAACCCTGACAATAACCACGAGCTAT

EST: gi|148960798|gb|EE011460.2|EE011460

EST:     CGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAG                         CTACAATGGCTGAACCCTG
genomic: CGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAGgtaaaattac ... caacatacagCTACAATGGCTGAACCCTG

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 4 RNA-Seq libraries.

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 82

TACTACTATTTCTGTTTTACTCGAAGACATACCAGGGGGGAGGTTGGGTCCGCAATGGATTCGGCCCACACCCCCAAGACTTCCTTTATTTGATGGGGAGgtaaaattac ... caacatacagCTACAATGGCTGAACCCTGACAATAACCACGAGCTATTATGGGATTATAGCATGTGTGCTGACACGAATCGAGGGGCTGCTATCCGAGATTTGATTGCAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107