ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGTGTCTGCAGTTTCATATGTTGGAAGCTATCTGTCCCGGGCAAGGTTCATTTCCGTAAATATAGTTGTTTCTGTACTCAAAAGgtggctaccctctgaacatacaaaatatttgttttgagcacctcacagtgtatctatgatttttgcatctgttctgtacatctgcgatttatgttatgttatgtgcttag

Basic information

species	Zea mays
transcript	GRMZM2G415846_T01
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G415846_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g47350.2 (Oryza sativa), 5'ss of exon 12

AGTGTCTGCAGTTTCATATGTTGGAAGCTATCTGTCCCGGGCAAGGTTCATTTCCGTAAATATAGTTGTTTCTGTACTCAAAAGgtggctacc-ctctg-aacatacaaa---atatttgttttgagcacctcacagtg-tatct-atgatttttgcatctgttctgtacatctgcgatttatgttatgttatgtgcttag
| ||||||||||||||||||||||||||||| |||| ||||||||||||||||| |   |||  || |||  | |||||||||||||| |    | ||| |   |    |   |||| ||| ||||| |        || ||| | |  || |||| |  | || ||  ||                              
AATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgttacgctgtagtgtctgcatccatatatgtcttgagtaatatggtttggtatttgaatatctttgtacttcttttg-gcag-----------------------------

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|211041735|gb|FL256640.1|FL256640

EST:     GTAAATATAGTTGTTTCTGTACTCAAAAG                         GCTAGTGGACTGGTGTGATTATTATTGTG
genomic: GTAAATATAGTTGTTTCTGTACTCAAAAGgtggctaccc ... atgtgcttagGCTAGTGGACTGGTGTGATTATTATTGTG

EST: gi|101383979|gb|EB814044.1|EB814044

EST:     TCCCGGGCAAGGTTCATTTCCGTAAATATAGTTGTTTCTGTACTCAAAAG                         GCTAGTGGACTGGTGTGATTATTATTGTGGCCATCAGCTGGACAATGGGGT
genomic: TCCCGGGCAAGGTTCATTTCCGTAAATATAGTTGTTTCTGTACTCAAAAGgtggctaccc ... atgtgcttagGCTAGTGGACTGGTGTGATTATTATTGTGGCCATCAGCTGGACAATGGGGT

EST: gi|93283859|gb|EB676123.1|EB676123

EST:     TCCCGGGCAAGGTTCATTTCCGTAAATATAGTTGTTTCTGTACTCAAAAG                         GCTAGTGGACTGGTGTGATTATTATTGTGGCCATCAGCTGGACAATGGGGT
genomic: TCCCGGGCAAGGTTCATTTCCGTAAATATAGTTGTTTCTGTACTCAAAAGgtggctaccc ... atgtgcttagGCTAGTGGACTGGTGTGATTATTATTGTGGCCATCAGCTGGACAATGGGGT

EST: gi|21843184|gb|BQ703750.1|BQ703750

EST:     TCCCGGGCAAGGTTCATTTCCGTAAATATAGTTGTTTCTGTACTCAAAAG                         GCTAGTGGACTGGTGTGATTATTATTGTGGCCATCAGCTGGACAATGGGGT
genomic: TCCCGGGCAAGGTTCATTTCCGTAAATATAGTTGTTTCTGTACTCAAAAGgtggctaccc ... atgtgcttagGCTAGTGGACTGGTGTGATTATTATTGTGGCCATCAGCTGGACAATGGGGT

EST: gi|26457293|gb|CA828876.1|CA828876

EST:     TCCCGGGCAAGGTTCATTTCCGTAAATATAGTTGTTTCTGTACTCAAAAG                         GCTAGTGGACTGGTGTGATTATTATTGTGGCCATCAGCTGGACAATGGGGT
genomic: TCCCGGGCAAGGTTCATTTCCGTAAATATAGTTGTTTCTGTACTCAAAAGgtggctaccc ... atgtgcttagGCTAGTGGACTGGTGTGATTATTATTGTGGCCATCAGCTGGACAATGGGGT

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: 42 (upstream exon), 49 (downstream exon)
Score: 235

AGTGTCTGCAGTTTCATATGTTGGAAGCTATCTGTCCCGGGCAAGGTTCATTTCCGTAAATATAGTTGTTTCTGTACTCAAAAGgtggctaccc ... atgtgcttagGCTAGTGGACTGGTGTGATTATTATTGTGGCCATCAGCTGGACAATGGGGTGACAGCAAATCCTATAAAGCACCAGCTATTTTATGCTAGCTGCCAG

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 172

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 160