ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCGATGAAgtgagtggaagatcttgcaattattgaggataattttgtattccgtagttttgtcaaagaaaatagtaatatggataatgctggtgtatgcgcag

Basic information

species	Zea mays
transcript	GRMZM2G030144_T02
intron #	12
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G030144_T03 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os06g07090.1 (Oryza sativa), 5'ss of exon 13

TAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCGATGAAgtgagtggaagatcttgcaattattgaggataattt-tgtattccgtagttttgtcaaagaaaatagtaatatggataatgctggtgtatgcgcag
|||| ||||||||||| || |||||||||||||||||||||||| | || || || || ||||||||||  ||||||||||| || ||||| || || ||||| |||  ||||  ||| |||  || || |  ||| | || |   |   ||| |  |||| |  | |||  | ||  |||||| ||||||  |||
TAAAGGAAATAGTTGCACAGAATAAAGGGAATACTGTGCTTGAACTACAACAGAGGTCAATTGAATTCAACTCCATTATACAGAGGCATCAGTCTATAAAgtgggtgacagattctgccattgctgtgggtgctttctctaatatatttgtttctgtaagatag-attaaccttgaggatgctgttgtatgaacag

upper sequence: GRMZM2G030144_T03 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA01G03890.1 (Glycine max), 5'ss of exon 13

TAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCGATGAAgtgagtggaagatcttgcaattattgaggataattttgtattccgtagttttgtcaaagaaaatagtaatatggataatgctggtgtatgcgcag
| ||||||||  |||  ||    |||||||    |||||| ||||||||||| ||| |||||||||||| ||| |||||   ||  ||||||   || | ||||| |  |  |  |    ||||| |   ||  |    ||   | | || |  ||        | |   ||    ||  |||   | || ||||
TCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGAGCTATTGAATTCAATTCGATTATTGCAAAGCATCAAAATATTAGgtgag-gttaattaatctgcttatt-atattatatcaagatcatggaattgtacca-------cactttcataagaaa--ctgtcat-tgtgcag

upper sequence: GRMZM2G030144_T03 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA02G03800.1 (Glycine max), 5'ss of exon 12

TAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCGATGAAgtgagtggaagatcttgcaattattgaggataattttgtattccgtagttttgtcaaagaaaatagtaatatggataatgctggtgtatgcgcag
| ||||||||  |||  ||    |||||||    |||||| ||||||||||| ||  |||||||||||||||| |||||   ||  ||||||   || | ||||  ||   ||    |   | || |   |   |    ||  || | || |         || | |   ||    ||  |||   | || ||||
TCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGGGCTATTGAATTCAGTTCGATTATTTCAAAGCATCAAAATATTAGgtga--ggttaattaatctgctttttatattgtatcaagatcacggaattgtac-------aacactttcataagaaa--ctgtcat-tgtgcag

upper sequence: GRMZM2G030144_T03 (Zea mays), 5'ss of exon 12
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 5'ss of exon 13

TAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCGATGAAgtgagtggaagatcttgcaattattgaggataattttgtattccgtagttttgtcaaagaaaatagtaatatggataatgctggtgtatgcgcag------------------------
|||  || ||| |||  ||   |||||| |    |||||||||||||||||| ||||| |||||||| | |||||||||    |  ||||||   || | ||  |     ||   |   | ||||  | || |||  ||  |   |   |||  |  ||||| | |  | ||| | |         | |    |                         
TAAGGGATATAATTGTCCAGTGTAAAGGAAGCCTTGTGCTTGAATTGCAGCAGAGATCCATTGAATTTAATTCCATTATTGGGAAGCATCAAAATATCAGgtatgcatttgaaagttgtaatattttgtatcattcagtgcttgatgtcttttccccagaaatttgccacatgtaaagcatatccatcttttaaagaagttctggatgaatgtctacag

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|71433260|gb|DR814310.1|DR814310

EST:     CAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCGATGAA                         ATCATCTTTGCTTGAACGGATGCCTGTATTGGATGAAGCTAATTATTTGGT
genomic: CAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCGATGAAgtgagtggaa ... gtatgcgcagATCATCTTTGCTTGAACGGATGCCTGTATTGGATGAAGCTAATTATTTGGT

EST: gi|67021834|gb|CO450583.1|CO450583

EST:     CAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCGATGAA                         ATCATCTTTGCTTGAACGGATGCCTGTATTGGATGAAGCTAATTATTTGGT
genomic: CAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCGATGAAgtgagtggaa ... gtatgcgcagATCATCTTTGCTTGAACGGATGCCTGTATTGGATGAAGCTAATTATTTGGT

EST: gi|67037313|gb|CO464163.1|CO464163

EST:     CAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCGATGAA                         ATCATCTTTGCTTGAACGGATGCCTGTATTGGATGAAGCTAATTATTTGGT
genomic: CAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCGATGAAgtgagtggaa ... gtatgcgcagATCATCTTTGCTTGAACGGATGCCTGTATTGGATGAAGCTAATTATTTGGT

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: 47 (upstream exon), 49 (downstream exon)
Score: 61

TAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCGATGAAgtgagtggaa ... gtatgcgcagATCATCTTTGCTTGAACGGATGCCTGTATTGGATGAAGCTAATTATTTGGTGAAGAGAGCTGCTTCTATACAGGCTGCAGTTCCATCTGTAAATTCTGCT

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 84

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98