ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtactgaacacaattagatgtcctactgaaaaaaaaatccattattacgtgcttgggttaactaatatcaatggcatctcttgtttcgggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATGAGCCGGCAGGTGAAAATTCACACGAGGCCTCTTCCGGACCTTGTCAAGA

Basic information

species	Zea mays
transcript	GRMZM2G055607_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G055607_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g44960.2 (Oryza sativa), 3'ss of exon 6

gtactgaa-cacaattagatgtcctactgaaaaaaaaatccattattacgtgcttgggttaactaatatcaatggcatctcttgtttcgggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATGAGCCGGCAGGTGAAAATTCACACGAGGCCTCTTCCGGACCTTGTCAAGA
||||| || || | | | |||   ||  |||  |    || || || ||   | | | ||  ||||    |||  |||||||        | | ||||||||| | || ||| ||||| |||||| | || |||||||| | |||| | ||| ||||||||||||||||||| || |||||||| | |||||||| ||
gtactaaaacatattcaaatgctgtaacgaagga----tcaatgataac---cctcgctttgctaa----aatatcatctct------atgaatgcagGCATTGTTCCAGGTACAAGAATTCCTCGGAGTTCCGGTGAGAAAGCTGGTCAGCAGGCAGGTGAAAATTCACACTAGTCCTCTTCCAGGCCTTGTCAGGA

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|71758717|gb|DR956654.1|DR956654

EST:     GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAAT                         GCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG
genomic: GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAATgtactgaaca ... gggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG

EST: gi|71305859|gb|DR789055.1|DR789055

EST:     GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAAT                         GCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG
genomic: GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAATgtactgaaca ... gggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG

EST: gi|84969427|gb|DW467864.1|DW467864

EST:     CAGCAACAGCAAT                         GCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG
genomic: CAGCAACAGCAATgtactgaaca ... gggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG

EST: gi|76911990|gb|DV164524.1|DV164524

EST:     GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAAT                         GCATTATCCCGGGTGCAAGAGTTCCTCGGGGTCCCGGTGAGGAGGCTGATG
genomic: GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAATgtactgaaca ... gggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG

EST: gi|71315790|gb|DR794540.1|DR794540

EST:     GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAAT                         GCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG
genomic: GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAATgtactgaaca ... gggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG

EST: gi|50330183|gb|CO525309.1|CO525309

EST:     GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAAT                         GCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG
genomic: GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAATgtactgaaca ... gggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG

EST: gi|31406257|gb|CD484989.1|CD484989

EST:     GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAAT                         GCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG
genomic: GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAATgtactgaaca ... gggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG

EST: gi|89247114|gb|DY618900.1|DY618900

EST:     GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAAT                         GCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG
genomic: GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAATgtactgaaca ... gggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG

EST: gi|71762875|gb|DR960812.1|DR960812

EST:     GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAAT                         GCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG
genomic: GTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAATgtactgaaca ... gggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATG

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), 44 (downstream exon)
Score: 33

CATCAGAAACATCGAGAAGGCCATCAGAGATTGCTTGGACCACTTCAAGAGTACGCGGCACATGATCCTCTATTATGAGGATATAATCAGCAACAGCAATgtactgaaca ... gggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATGAGCCGGCAGGTGAAAATTCACACGAGGCCTCTTCCGGACCTTGTCAAGA

Block sizes: 39 (upstream exon), 43 (downstream exon)
Score: 13

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 57

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 193

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tattacgtgcttgggttaactaatatcaatggcatctcttgtttcgggcacgcagGCATTATCCCGGGTGCAAGAGTTCCTCAGGGTCCCGGTGAGGAGGCTGATGAGCCGGCAGGTGAAAATTCACACGAGGCCTCTTCCGGACCTTGTCAAGA