ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCGgtacgtaatttagataaaagctacgtgcacaatgacaaatttatttagtttctaatatttccatcactttacag

Basic information

species	Zea mays
transcript	GRMZM2G324540_T02
intron #	13
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G324540_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 12

TCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCGgtacgtaatttagataaaagctacgtgcacaatgacaaatttatttagt-ttctaatat---ttccatcactttacag
|||||||| |||||||||||||| ||||| |||||||| ||||||||||| ||||||||||||||||||||||| |||||| | |  |      |  || |  |||| ||||   ||||| |||  | |||| ||||   |  ||||||| |||||
TCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatctctccatagtgcaatctgcaaaatgttgaatttcttttttattctgatatatgtatcatcactgtacag

upper sequence: GRMZM2G324540_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT2G33340.1 (Arabidopsis thaliana), 5'ss of exon 14

TCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCGgtacgtaatttagataaaa-gctacgtgcacaatgacaaatttatttagtttctaatatttccatcactttacag--------------
 ||||||| || |||||||| || ||    ||   ||| || ||||| |||||||||||||||||||||||||| |||||  ||| |||  | ||||  | |   |    |  |||  || | |||   |   ||   |   |  ||||                  
GCAAATGTGGCTAAGTTTGATGGACACACTGGGGAAGTTACAGCTATATCTTTCTCTGAAAATGGTTACTTCCTCGCGgtgagtactttgaacaaaatacgagaagagagaatacagcttaagttatgcttacatgaatgattttctttttgtcctggaattgacag

upper sequence: GRMZM2G324540_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv05s0049g01840.t01 (Vitis vinifera), 5'ss of exon 14

TCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCGgtacgtaattt---agataaaagc---tacgtgcacaa-tgacaaatttatttagtttctaatatttccatcactttacag
 ||||||| ||||  ||||| || || || ||  | || |||||||| |||||||| ||||||||||||||||| |||||| ||  |||   |  || |||    || |||   || ||||| |  | | |  ||| | ||  ||  ||   ||||   
GCAAATGTGGCAAGATTTGACGGGCACGTTGGGGCTGTAACTGCTATATCTTTCTCAGAAAATGGTTACTTCCTTGCGgtatgtgttttcctaattagaagtgtatatgtgaggaagtgacatacatttctgattttttatgcttg-atgtttttag--

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|33096397|gb|CF056391.1|CF056391

EST:     TCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG                         ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTTCGTAAATTAAGAAAT
genomic: TCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCGgtacgtaatt ... cactttacagACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTTCGTAAATTAAGAAAT

EST: gi|60337485|gb|DN204458.1|DN204458

EST:     TCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG                         ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTT
genomic: TCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCGgtacgtaatt ... cactttacagACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTT

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: 173

TCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCGgtacgtaatt ... cactttacagACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTTCGTAAATTAAGAAATTTTAGGACTTTCTCTCCCTATGATTTGGACACGCCAACCAATACTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 82