ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAATGGTTTCGATGGCACCGATACACATTACTTCCATGGTGGTCCACGAGGCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatgtgcagaatgtattagctaatagttcatatttattttctatacacacataacaattcattttgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G073054_T01
intron #	12
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA19G37750.2 (Glycine max), 5'ss of exon 12

GAATGGTTTCGATGGCACCGATACACATTACTTCCATGGTGGTCCACGAGGCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatg----tgcagaatgtattagctaatagttcatatttattttctatacacac------ataacaattcattttgtgcag------------
|||    || ||||| || |||   ||||||||||||  |||  |||||||  ||||||||||||||||||||||||| || || ||||| || ||||||||| ||  ||       |||||  ||| ||  |   |    |   | |||||||||   |      | |  || | | ||  |  |             
GAACATGTTTGATGGAACTGATGGTCATTACTTCCATCCTGGGTCACGAGGTTATCATTGGATGTGGGATTCTCGCCTTTTTAACTATGGAAGCTGGGAAgtaagtgctggctccaaagaattcattggcatagtatctgaaaaaaatttctataccttctgttcaacagtaaatgacttactttaattcttaatttag

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA03G35020.1 (Glycine max), 5'ss of exon 12

GAATGGTTTCGATGGCACCGATACACATTACTTCCATGGTGGTCCACGAGGCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatg----tgcagaatgtattagctaatagttcatattta--ttttctatacacac------ataacaattcattttgtgcag------------
|||    || ||||| || |||   ||||||||||||  |||  |||||||  ||||||||||||||||||||||||| || || || || || ||||||||| ||  ||       |||||  ||| ||  ||||||  |    |  |||||  |||   |      | |  || | | ||  |  |             
GAACATGTTTGATGGAACTGATGGTCATTACTTCCATCCTGGGTCACGAGGTTATCATTGGATGTGGGATTCTCGCCTTTTTAACTACGGAAGCTGGGAAgtaagtgctggctccaaagaattcattggc--atagtttctgacaaaattttccgtaccttctgttcaacagtaagtgacttactttaattcttaatttag

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT2G36390.1 (Arabidopsis thaliana), 5'ss of exon 12

GAATGGTTTCGATGGCACCGATACACATTACTTCCATGGTGGTCCACGAGGCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatgt---gcagaatgtattagctaatagttc---atatttattttctatacacacataacaattcattttgtgcag------------------------------------
| |    || ||||| || |||   || || |||||   |||  | || ||  |||||||||||||||||||||| || |||||||| || || |||||||||||||   |   | ||| |  ||     |||| ||      |    |||  | ||  | |||     |   || |||   |                                    
GGACATGTTTGATGGTACTGATGGTCAATATTTCCACTCTGGATCGCGTGGTTATCATTGGATGTGGGATTCTCGTCTTTTCAATTACGGAAGCTGGGAAgtatgtctctttccgtagagttgatattgcaatatttatgggaaagcctttagtgtagccccatgctggtg-gttatgtctggtccttgtgtattgacgtttggtccttgtgtatttag

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 5'ss of exon 12

GAATGGTTTCGATGGCACCGATACACATTACTTCCATGGTGGTCCACGAGGCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatgt----gcagaatgtattagctaat--agttcatatttattttctatacacaca--------taacaattcattttgtgcag---------
|||    || ||||| || ||| | || || || ||   ||| || || ||  | ||||||||||||||||| || || |||||||||||||| |||||||||||| |  |    |   | | || | |  |||  |||  | ||  |  |||  ||  |||          |||| |   |||||  |           
GAACATGTTTGATGGAACTGATGCTCACTATTTTCACTCTGGACCTCGGGGATACCATTGGATGTGGGATTCACGACTTTTCAATTATGGGAGCTGGGAAgtatgtaactttttcgtgaattttaatcgaaaatgtagtgaacatacaacttccttaagcactatcagttccaacagtctcttttgatcttttctaacag

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 5'ss of exon 12

GAATGGTTTCGATGGCACCGATACACATTACTTCCATGGTGGTCCACGAGGCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatgtgcag--aatgtattagctaatagttcatatttattttctatacacacataacaattcattttgtgcag--------------------
 ||  | || ||||| || ||||  || || ||||||  |||  || | ||  | || |||||||||||||||||||| || ||||| || || ||||||||||||  | ||  |  || || | |   ||||||     |||    | ||| | |  ||     ||  || |  | |                     
AAACAGGTTTGATGGAACTGATAGTCACTATTTCCATTCTGGATCAAGGGGTTACCACTGGATGTGGGATTCTCGCCTTTTTAATTACGGAAGCTGGGAAgtatgtgctttgatgccaaagt-tcaagaaatagtgt---tttgccctttatgctcttattgttttttgttgtagggattaattgtctctttgttttag

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|67035192|gb|CO463725.1|CO463725

EST:     GCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAA                         GTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAA
genomic: GCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatg ... ttttgtgcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAA

EST: gi|101386689|gb|EB815361.1|EB815361

EST:     GCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAA                         GTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAA
genomic: GCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatg ... ttttgtgcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAA

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: 536

GAATGGTTTCGATGGCACCGATACACATTACTTCCATGGTGGTCCACGAGGCCATCATTGGATGTGGGATTCTCGCCTATTCAATTATGGGAGTTGGGAAgtatgtcatg ... ttttgtgcagGTTTTGAGATTTCTATTGTCAAATGCGAGATGGTGGCTTGAAGAATATAAATTTGATGGGTTTCGATTTGATGGGGTGACCTCCATGATGTATACTCACC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 127

Block sizes: 48 (upstream exon), 36 (downstream exon)
Score: 6