ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacatacagaacactcttgtggtattttattcaccgtcaagaactatatttgatgatgacccttttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG

Basic information

species	Zea mays
transcript	GRMZM2G123732_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G123732_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g54920.1 (Oryza sativa), 3'ss of exon 4

gtacatacagaacactcttgtggtatttta------------ttcaccgtc-aagaactatatttgatgatgacccttttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG
||| | ||  | | || |||| |||||| |            |||| | |   ||| |  |||||||  |      | ||| |  ||||| || |||||||| |  ||||| |||||||| ||||||||||| || || |||||||||||| |||| ||||||||||||
gtaaacact-agcccttttgtagtatttcagtgtgatgctaattcaacatttgagagcattatttgagcaaatatttcttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG

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|211483660|gb|FL342584.1|FL342584

EST:     TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATGTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT

EST: gi|211118164|gb|FL349423.1|FL349423

EST:     TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATGTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT

EST: gi|71323879|gb|DR798616.1|DR798616

EST:     TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATG                         -TTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTC-T
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT

EST: gi|211474975|gb|FL438616.1|FL438616

EST:     TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCC
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT

EST: gi|74244183|gb|DT652097.1|DT652097

EST:     TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTC
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATA-A-TCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTC

EST: gi|33092349|gb|CF052343.1|CF052343

EST:     TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATGTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT

EST: gi|93011727|gb|EB637247.1|EB637247

EST:     TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT

EST: gi|32933373|gb|CF038185.1|CF038185

EST:     TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATGTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT

EST: gi|74244184|gb|DT652098.1|DT652098

EST:     TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATATAATCTCACAATCGTATG
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATA-A-TCTCACAATCGTATG

EST: gi|32934905|gb|CF039717.1|CF039717

EST:     TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATG                         GTTATATAATGTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 44

AACCAGCATACTACAACTATGTATGTGCGATGTTGCTATTGAATGGTGTATCACTGTTTGGATGTTTCCTTGTTGCAAGTGGAGCTGGATTTGGTTTATGgtacatacag ... tttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG

Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 43

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 51

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 39

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtggtattttattcaccgtcaagaactatatttgatgatgacccttttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG