ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTGCTGACTCCCTGTTGCTGTTTCTTGGCCTTGGTTGTGGTGAATCCAGGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctttgagctcttgatttggattccagttgtgcttagggtattttgtcatgagattggggatattgtttggaagaaagtgataattcatatcct...

Basic information

species	Zea mays
transcript	GRMZM2G052713_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G052713_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g10560.1 (Oryza sativa), 5'ss of exon 3

GTGCTGACTCCCTGTTGCTGTTTCTTGGCCTTGGTTGTGGTGAATCCAGGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctttgagctcttgatttggattccagttgtgc----ttagggtattttgtcatgagattggggatattgtttggaagaaagtgataattcatatcct
                                                 ||||||||||| |||||||||||||| |||||||||||||||||||| |||||| || ||| || || ||  |||||     |||| |||     |  ||   ||  |  | |||        |     ||    || ||  |   |  |   | 
-------------------------------------------------GTGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt-gatcttttattttgggggg-agttatgcgattcttaggcgattcatggt-agaagaaaaccaagagctgcgtaaaggtctttgcttttgctc-

upper sequence: GRMZM2G052713_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv18s0001g14240.t01 (Vitis vinifera), 5'ss of exon 4

GTGCTGACTCCCTGTTGCTGTTTCTTGGCCTTGGTTGTGGTGAATCCAGGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctttgagctcttgatttggattccagttgtgcttagggtattttgtca-tgagattgggg-atattgtttggaagaaagtgataattcatatcct--
                                                 || || ||  | || ||||||||||| ||||||||||| |||||||| |||||   | ||||   |||    ||||| ||           ||||| |   ||  | ||  |||     || ||||||  |        | ||||  ||   |  
-------------------------------------------------GTTCACCGATTGGTTGTCAACCGGGATCCCAAGTTCACTAACTTCGTTGAGgtattttcttt---ctcgacgtttggcttgtgagaaaatctagggaacaatgcaaatgcaattattttatgttgtttc-attttcacaagaatttttagaattg

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|60351820|gb|DN218793.1|DN218793

EST:     GCATCNGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: GCATC-GGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT

EST: gi|32943128|gb|CF047947.1|CF047947

EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACTAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT

EST: gi|60394275|gb|DN227145.1|DN227145

EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT

EST: gi|60352004|gb|DN218977.1|DN218977

EST:     TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAG                         TTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACNNNNNNNCTCT
genomic: TGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCT

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: 49 (upstream exon), 49 (downstream exon)
Score: 229

GTGCTGACTCCCTGTTGCTGTTTCTTGGCCTTGGTTGTGGTGAATCCAGGTGCATCGGCTCGTGGTCAACCGGGACCCCAAGTTCACCAACTTCGTCGAGgtgggtgctt ... tctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCTATATGTGTGGACATCACCGACAACGAATTGGCATACTTGGAATGTATCC

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 319

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 190