ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGAGGCTGAAGTGCGGATTGCAGCTGCTGGAAAAGTTACAAAATTCTGCAAAATATTAAACCCACAAATTGCAATTGAACATATTCTTCCGTGTATCAAGgtgtgtttaagcattgcacaaacactattgagctctgcaccaatattcagtggttaacttgtgccttttgtactcatag

Basic information

species	Zea mays
transcript	GRMZM2G102858_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 6

TGAGGCTGAAGTGCGGATTGCAGCTGCTGGAAAAGTTACAAAATTCTGCAAAATATTAAACCCACAAATTGCAATTGAACATATTCTTCCGTGTATCAAGgtgtgttt------------aagcattgcaca--aacactattgagc-tctgcaccaatattcagtggtt--aacttgtgccttttgtactcatag------------------------------------------
||||||||||||||| || ||||||||||||||||| || || || |||   || ||||| ||| |  || ||||| | ||||||||| | ||| | ||||| |   |            ||  ||  ||||  |  | || |||   | | ||      ||   |||||     | ||   ||  |||  |  |                                           
TGAGGCTGAAGTGCGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTAAATCCAGATCTTTCAATTCAGCATATTCTTTCTTGTGTGAAGgtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcag

upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 5'ss of exon 6

TGAGGCTGAAGTGCGGATTGCAGCTGCTGGAAAAGTTACAAAATTCTGCAAAATATTAAACCCACAAATTGCAATTGAACATATTCTTCCGTGTATCAAGgtgtgt--ttaagcattgcacaaacact----attgagctctgcaccaatat----tcagtggttaacttg--tgccttt---tgtactcatag
|||||| ||||| ||||| |||||||||||||||||||| || || ||    || ||||||||  || | || ||  | || |||||||| ||| | |||||      ||||| |  |       | |    |||  ||   | ||||| ||    || ||| ||     |  | ||| |   | ||| | |||
TGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTAAACCCTGAACTCGCTATCCAGCACATTCTTCCCTGTGTAAAGgtacacacttaagaagagtgtgttgatttcatattatgcaaaggaccaaaatactgtcggtgtttgctaagcttacctataaatctacacgtag

upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 5'ss of exon 5

TGAGGCTGAAGTGCGGATTGCAGCTGCTGGAAAAGTTACAAAATTCTGCAAAATATTAAACCCACAAATTGCAATTGAACATATTCTTCCGTGTATCAAGgtgtgtttaagcattgcacaaacactattgagctctgcacca-atattcagtggttaacttgtgc-cttttgtactcatag--------------------------------------------
|||||||||||| || || ||||||||||| ||||| || ||||||||  | || ||||| ||| || |||||||| | ||||||||||| ||| | ||||||         |||  |  |    |  |  |   |  |  |  | | |  | ||| ||       || |||  || ||                                              
TGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTAAATCCAGAACTTGCAATTCATCATATTCTTCCCTGTGTAAAGgtgctcacgtttattaaaagagtgtttctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaatatttggtgatgtcattttgtag

upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 7

TGAGGCTGAAGTGCGGATTGCAGCTGCTGGAAAAGTTACAAAATTCTGCAAAATATTAAACCCACAAATTGCAATTGAACATATTCTTCCGTGTATCAAGgtgt----gtttaagcattgcacaaacactattgagctctgcaccaatattcagtggttaacttgtgccttttgtactcatag-----------------------------------------------------------
|||||||||||| || || |||||||| |||||||| |||||||| |||   || || |||||| || |||||||| | ||||||||||| ||| | ||||| |    | ||    |      ||     |||  ||| || |    |  | |  || | || ||      || || | |                                                              
TGAGGCTGAAGTACGCATAGCAGCTGCAGGAAAAGTAACAAAATTTTGCCGGATTTTGAACCCAGAACTTGCAATTCAGCATATTCTTCCTTGTGTGAAGgtatacatgcttgcaaaagttttaagtttcattatgctatgaa--gtttcttatgggcttacatggtggggttctatttaccactgcttatctgtcatctgtcttaaaatttgtgactagattagaaaatgtccttctgcag

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|18383985|gb|BM417185.1|BM417185

EST:     AAATATTAA-CCCACAAATTGCAATTGAACATATTCTTCCGTGTATCAAG                         GAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTT
genomic: AAATATTAAACCCACAAATTGCAATTGAACATATTCTTCCGTGTATCAAGgtgtgtttaa ... gtactcatagGAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTT

EST: gi|6194513|gb|AW146617.1|AW146617

EST:     AAATATTAAACCCACAAATTGCAATTGAACATATTCTTCCGTGTATCAAG                         GAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTT
genomic: AAATATTAAACCCACAAATTGCAATTGAACATATTCTTCCGTGTATCAAGgtgtgtttaa ... gtactcatagGAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTT

EST: gi|32851132|gb|CD990813.1|CD990813

EST:     AAATATTAAACCCACAAATTGCAATTGAACATATTCTTCCGTGTATCAAG                         GAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTT
genomic: AAATATTAAACCCACAAATTGCAATTGAACATATTCTTCCGTGTATCAAGgtgtgtttaa ... gtactcatagGAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTT

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: 182

TGAGGCTGAAGTGCGGATTGCAGCTGCTGGAAAAGTTACAAAATTCTGCAAAATATTAAACCCACAAATTGCAATTGAACATATTCTTCCGTGTATCAAGgtgtgtttaa ... gtactcatagGAATTATCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCATCGGTTATTATGGGAATGGCTCCTGTATTGGGAAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124