ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTTTCGCTATGTAGCACATGTAATTTACAAGAGAGAAATAGAGGGTCCTCTTGACTTCAGAATCCTCCGAAATTCAGATTTTCGTGAAATTACACTGGAGgtaaactcattcccttgatgatcatggaaaaccagtaattttcacctagcttgagtgattgtatgtataacaattagcaaatgctgcgtgtgctagcag

Basic information

species	Zea mays
transcript	GRMZM2G171998_T01
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G171998_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g53750.2 (Oryza sativa), 5'ss of exon 8

CTTTCGCTATGTAGCACATGTAATTTACAAGAGAGAAATAGAGGGTCCTCTTGACTTCAGAATCCTCCGAAATTCAGATTTTCGTGAAATTACACTGGAGgtaaactcattcccttgatgatcatggaaaaccagtaattttcacctag------cttgagtga--ttgtatgtataacaattagcaaatgctgcgtgtgctagcag
||||||  |||  ||||||||  | | | | ||| |||| || ||  |  |||| ||||||||| | ||||||||||||||||||||  ||||||||||||| || ||||  |||  || ||  |||    |    |||| || | ||        |  ||||   ||  ||  ||      || |   || || ||       |||
CTTTCGACATGCGGCACATGTTCTCTTCGATAGAAAAATTGAAGGATCAGTTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAGgtgaattcat--cctgcatcatgttggcctgctttcaattctctcttaagcatgattcaagtggccttagattaattttgtataacgtgtgttgtgttaatgcacag

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|6865211|gb|AW360561.1|AW360561

EST:     TGACTTCAGAATCCTCCGAAATTCAGATTTTCGTGAAATTACACTGTTAG                         GTGGAGGGCAAACCTGTTTTGAA
genomic: TGACTTCAGAATCCTCCGAAATTCAGATTTTCGTGAAATTACACTGG-AGgtaaactcat ... gtgctagcagGTGGAGGGCAAACCTGTTTTGAA

EST: gi|32936523|gb|CF041342.1|CF041342

EST:     TTGACTTCAGAATCCTCCGAAATTCAGATTTTCGTGAAATTACACTGGAG                         GTGGAGGGCAAACC
genomic: TTGACTTCAGAATCCTCCGAAATTCAGATTTTCGTGAAATTACACTGGAGgtaaactcat ... gtgctagcagGTGGAGGGCAAACC

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: 19

CTTTCGCTATGTAGCACATGTAATTTACAAGAGAGAAATAGAGGGTCCTCTTGACTTCAGAATCCTCCGAAATTCAGATTTTCGTGAAATTACACTGGAGgtaaactcat ... gtgctagcagGTGGAGGGCAAACCTGTTTTGAAGTTTGCACTTTGTTATGGATTCAGGAACCTGCAGAATGTTGTTAGGAAGATTAAGATGGGAAAATGTGAATACCACT

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 58

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 76