ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCTTGGTGTTGGTGTTGCAACTGTAACTGATCTGCAACTCAACGTTATGGGATCTGTACTGTCCCTACTGGCAATCATCACAACCTGCATCGCTCAGATCgtatccttttgattgtacattacccactattttttttatgtggcatatctgtcacagtatccagaaccatttgcatacaccaaactttgcatttgccactaaagcatcctgtaatttgagtattagtgttctgtggcgtataacttgagtccttaacaagccatcag

Basic information

species	Zea mays
transcript	GRMZM2G116053_T01
intron #	5
splice site	5'
intron type	U12 (go to U12 genes for details)

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G116053_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g07310.1 (Oryza sativa), 5'ss of exon 5

TCTTGGTGTTGGTGTTGCAACTGTAACTGATCTGCAACTCAACGTTATGGGATCTGTACTGTCCCTACTGGCAATCATCACAACCTGCATCGCTCAGATCgtatccttttgattgtacattac-ccactattttttttatgtggcatatctgtcacagtatccagaaccatttgcatacaccaaactttgcatttgccactaaagcatcctgtaatttgagtattagtgttctgtggcgtataacttgagtccttaacaagccatcag
| |||||||||| ||||||||||| ||||| ||||| || || | | |||||||||| |||||  | || |||||||| ||||||||||| ||||| |||||||||||||||  | |  | |        ||| |   | ||   || | || || |  |||   |          || |  ||||  | ||  ||  | |                                                                   
TTTTGGTGTTGGAGTTGCAACTGTGACTGACCTGCAGCTTAATGCTGTGGGATCTGTCCTGTCTTTGCTCGCAATCATTACAACCTGCATTGCTCAAATCgtatccttttgacagcaagtgatattttcgtttatgaaacgttatatgtttgccaaataatctgcacatcaccatctaaagaaaacagtccacatgt-att-------------------------------------------------------------------

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|44901544|gb|CK828089.1|CK828089

EST:     GATCTGTACTGTCCCTACTGGCAATCATCACAACCTGCATCGCTCAGATC                         ATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCAACACAGCTCCTG
genomic: GATCTGTACTGTCCCTACTGGCAATCATCACAACCTGCATCGCTCAGATCgtatcctttt ... aagccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCAACACAGCTCCTG

EST: gi|60398713|gb|DN231529.1|DN231529

EST:     GATCTGTACTGTCTGTACTGGCAATCATCACAACCTGCATCGCTCAGATC                         ATGACAAATACAATACAGAAGAAGTTCA
genomic: GATCTGTACTGTCCCTACTGGCAATCATCACAACCTGCATCGCTCAGATCgtatcctttt ... aagccatcagATGACAAATACAATACAGAAGAAGTTCA

EST: gi|67020057|gb|CO448806.1|CO448806

EST:     GATCTGTACTGTCCCTACTGGCAATCATCACAACCTGCATCGCTCAGATC                         ATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCGACACAGCTCCTG
genomic: GATCTGTACTGTCCCTACTGGCAATCATCACAACCTGCATCGCTCAGATCgtatcctttt ... aagccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCAACACAGCTCCTG

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), 48 (downstream exon)
Score: 153

TCTTGGTGTTGGTGTTGCAACTGTAACTGATCTGCAACTCAACGTTATGGGATCTGTACTGTCCCTACTGGCAATCATCACAACCTGCATCGCTCAGATCgtatcctttt ... aagccatcagATGACAAATACAATACAGAAGAAGTTCAAGGTATCTTCAACACAGCTCCTGTACCAGTCATGCCCATACCAGGCATTGACGTTGTTCCTTGTCGGTCCAT

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 145

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218