ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatcaatgtttaattattgtgctttgttcatacttcacagtataaatacttaagatacgtcaagttatgctatccatgtgctagccttatttactatattccaattaatttgttgctactctatgtttactaagtagttttttggttaaatttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATCGAAAACTCGGC

Basic information

species	Zea mays
transcript	GRMZM2G044180_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G044180_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 3

gtatcaatgtttaattattgtgctttgttcatacttcacagtataaatacttaagatacgtcaagttatgctatccatgtgctagccttattt--actatattcc-aattaatttg---ttgctactctatgtttactaagtagttttttggttaaatttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATCGAAAACTCGGC
                                                                 ||||  ||| | | ||||| | || |||  | ||||||   || |||||||   ||||| |  ||  ||| |||||| | ||| ||      | ||| || |||||||||||||||||||| ||||||||||| ||| ||||||||||| ||||| ||||||||||||| ||||| || ||||||||||||  || ||||  |
----------------------------------------------------------------tttat-ttattcgtctgctacctttgtttcaaatatatttttaaataatttggtattgctgccttacattttctaagtgggtttatgtgc---tgtttttgcagGGAGTTTTTGGTTGATCTCATGGCTGCTCCCGGTACTCTTATTCCATCAGATGTCTTAAGTTGGAAGGGCAACTCATTAAATTCTAATGCAAGACTCACC

upper sequence: GRMZM2G044180_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 4

gtatcaatgttta-attattgtgctttgttcatacttcacagtataaatacttaagata-cgtcaagttatgctatccatgtgctagccttatt--tactatattccaattaatttgttgctactct--atgtttactaagtagttttttggtta---aatttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCT---AATCGAAAACTCGGC
||       |||| ||  ||||  |||  |  || ||   | | ||   | ||| |  | | |    |     | |  |||        | |||  | | ||  |   ||   | |     ||| |   | |||||    || ||  |    |     | | |   |  |||||||||||||||||||| ||||||||||| ||  | ||||| ||||| ||||| |||||    || |  | | | || ||  ||   ||||  ||  |    
gttaaggcttttacatctttgtatttttcttgtatttgttaatttactaatttatgtaatcattggatacaaatttatatgcatggaaatgattgatgcgatcattggatatctctaagtttacccggaaagtttatgttgtggtactgacatctcctactctgctttcagGGAGTTTTTGGTTGATCTCATGGCTGCTCCAGGGACACTTATCCCAGCTGATATTTTAAGCACCAAGGATAGTGCCTTTAAGCCTTACAATCCCAAGATT---

upper sequence: GRMZM2G044180_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 3

gtatcaatgttta-attattgtgctttgttcatacttcacagtataaatacttaag-atacgtcaagttatgctatccatgtgctagccttatttactatattccaattaat---ttgttgctactctatgtttactaagtagttttttggt-------taaatttttctgt---------agGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCT---AATCGAAAACTCGGC
||       |||| ||  ||||  |||  |  || ||   | | ||   | ||| | || | |     |||  | | ||||     |   | ||    ||  |  |   |||   | | ||   || || ||| ||  || |  ||| || |       | |  | | ||           |||||||||||||||||||| ||||||||||| ||  | ||||| ||||| ||||| |||||    || |  | | | || || |||   ||||  ||  |    
gttaaggcttttacatctttgtatttttcttgtatttgttaatttactaatttatgtatgcatgtgtatatcatgtgcatgcctatgtactcttgtaaatggttgaggcaatcattggatgtctctataagttcacccagaaagtttatgttgtggtactgacgtctcctactctgctttcagGGAGTTTTTGGTTGATCTCATGGCTGCTCCAGGGACACTTATCCCAGCTGATATTTTAAGCACCAAGGATAGTGCCTTTAAGTCTTACAATCCCAAGATT---

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|149102684|gb|EE288035.2|EE288035

EST:     GGTGGTGATGACGACGATGCTATAAACATAATTAAGATGGACAATGAAAG                         GGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGA
genomic: GGTGGTGATGACGACGATGCTATAAACATAATTAAGATGGACAATGAAAGgtatcaatgt ... ttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGA

EST: gi|148980136|gb|EE026970.2|EE026970

EST:     GGTGGTGATGACGACGATGCTATAAACATAATTAAGATGGACAATGAAAG                         GGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGA
genomic: GGTGGTGATGACGACGATGCTATAAACATAATTAAGATGGACAATGAAAGgtatcaatgt ... ttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGA

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), 49 (downstream exon)
Score: 162

CCTATAGTGTTGGGATTCCATGCAAACTTGTCAAAGGGAGCAATTATACTGGTGGTGATGACGACGATGCTATAAACATAATTAAGATGGACAATGAAAGgtatcaatgt ... ttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATCGAAAACTCGGC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 133

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aatttgttgctactctatgtttactaagtagttttttggttaaatttttctgtagGGAGTTTTTGGTTGATCTGATGGCTGCTCCTGGTGCTCTTATTCCAGCAGATATCTTAAGTTGGAAAGGCAATTCGTTAAATTCTAATCGAAAACTCGGC