ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTCCTTCCAGCTTGTGTTTGCACCAATTGATGAGCATTTCCCAGATGATGCTCCATTGATTTCTTCTGGCTTTCGTGTCATACCACTTGATGTGAAAACAgttaagcattgccaacaacattaccttttccctttttttccttgcttgggcagccgcttcatttccttgtctattatgtttataattatccttaacatgt...

Basic information

species	Zea mays
transcript	GRMZM2G109987_T05
intron #	14
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G109987_T05 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os03g01890.1 (Oryza sativa), 5'ss of exon 15

---CTCCTTCCAGCTTGTGTTTGCACCAATTGATGAGCATTTCCCAGATGATGCTCCATTGATTTCTTCTGGCTTTCGTGTCATACCACTTGATGTGAAAACAgttaagcattgccaa---caacattaccttttccctttttttccttgcttgggcagccgcttcatttccttgtctattatgtttataattatccttaacatgt
   |||||| ||||||||||||||||| ||||||||   ||||||||||||  |||||||||||||||||||||| ||||| |||||||||||| ||||||||||||||   ||||||   | | ||||| || ||| ||    |  |||  ||  |    | | ||| |     |   ||    ||  | | |||  | |     
ATCCTCCTTTCAGCTTGTGTTTGCACCGATTGATGA---TTTCCCAGATGAAACTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACAgttaagtgctgccaaattccaaattacattatccattaccctt-ttgactgttccctaggtccatatgtgctttatttgctgttgcattaatctgtgatga--

upper sequence: GRMZM2G109987_T05 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA12G08080.1 (Glycine max), 5'ss of exon 14

CTCCTTCCAGCTTGTGTTTGCACCAATTGATGAGCATTTCCCAGATGATGCTCCATTGATTTCTTCTGGCTTTCGTGTCATACCACTTGATGTGAAAACAgttaagcattgc-caacaacattaccttttccct--ttttttccttgcttgggcagccgcttcatttccttgtctattatgtttataattatc-cttaacatgt
 |  |   ||||||| ||||| |||||||||||    ||||| |||||||||||||||||| ||||||| || ||  | || ||| | |||   ||| ||||||||  |||  |  |   |||    ||||  |  | | | || |||||    |     ||||  || ||   | ||    | |   ||| | | |   ||| 
TTGTTCTGAGCTTGTATTTGCTCCAATTGATGAAATGTTCCCCGATGATGCTCCATTGATTCCTTCTGGTTTCCGCATTATCCCATTAGATTCAAAACCAgttaagttttgttcctctgtattttgctttctataatctctaccgtgctt---tatttttttcagctctttacatctt-cactcaagcttagcgcatgtaatga

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|31350140|gb|CD434497.1|CD434497

EST:     CTCCATTGATTTCTTCTGGCTTTCGTGTCATACCACTTGATGTGAAAACA                         GATGGTGTATCCTCTGGTAGGACGCTAGATTTGGCATCTAGTCTTGATGTG
genomic: CTCCATTGATTTCTTCTGGCTTTCGTGTCATACCACTTGATGTGAAAACAgttaagcatt ... tctcatgcagGATGGTGTATCCTCTGGTAGGACGCTAGATTTGGCATCTAGTCTTGATGTG

EST: gi|50334712|gb|CO529838.1|CO529838

EST:     CTCCATTGATTTCTTCTGGCTTTCGTGTCATACCACTTGATGTGAAAACA                         GATGGTGTATCCTCTGGTAGGACGCTAGATTTGGCATCTAGTCTTGATGTG
genomic: CTCCATTGATTTCTTCTGGCTTTCGTGTCATACCACTTGATGTGAAAACAgttaagcatt ... tctcatgcagGATGGTGTATCCTCTGGTAGGACGCTAGATTTGGCATCTAGTCTTGATGTG

EST: gi|60336823|gb|DN203796.1|DN203796

EST:     CTCCATTGATTTCTTCTGGCTTTCGTGTCATACCACTTGATGTGAAAACA                         GATGGTGTATCCTCTGGTAGGACGCTAGATTTGGCATCTAGTCTTGATGTG
genomic: CTCCATTGATTTCTTCTGGCTTTCGTGTCATACCACTTGATGTGAAAACAgttaagcatt ... tctcatgcagGATGGTGTATCCTCTGGTAGGACGCTAGATTTGGCATCTAGTCTTGATGTG

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), 46 (downstream exon)
Score: 175

CTCCTTCCAGCTTGTGTTTGCACCAATTGATGAGCATTTCCCAGATGATGCTCCATTGATTTCTTCTGGCTTTCGTGTCATACCACTTGATGTGAAAACAgttaagcatt ... tctcatgcagGATGGTGTATCCTCTGGTAGGACGCTAGATTTGGCATCTAGTCTTGATGTGGGCTCTGCTGCACCCCAAGCCTCAGGGGAATCTCCAGATGACTGCAGTT

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 61

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76