ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatagccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgttaatttattgagcag

Basic information

species	Zea mays
transcript	GRMZM2G062042_T02
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 26

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatagccagacagtcgtgcaattcctatcgctaccgcttttaattt-aataacatgtgtt---aatttattgagcag
| | |||||||| |||||||| ||||| ||||| || ||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||||||||||||   |  | |  || |     |  |  ||   ||  | |  ||     ||||| ||| ||||||   ||     |||   |||| |||
ATCTTTGAATGAGCTTTATGTTGAAGAGGAGGATTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAGAAGgtaaagcgattagatgattgtactgct-tattgatgttatttttccttttttttttattttgaataactaatggctggaatgccttgatcag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 26

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatag--ccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgtt---aatttattgagcag
||| |||||||| |||||||| ||||| |||||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||| ||||||||   |  |||  || |  |     | |  ||  |||  |  |  |     |||   || ||||||   ||     |||   |||| |||
AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgattatatgattgtactgcttattgatgttattttt-ccttttttattttattttgaataactaatggctggaatgccttgatcag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 26

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaat-------agccagacagtc-gtgcaattcctatcgctaccgcttttaatttaataacatgtgttaatt--tattgagcag----------------------
 || ||||||||| ||||||  || || || ||||| || ||||||||||||||| | ||  ||||||| ||||| || ||||| |||||||| |||||||| ||    |  ||   |       |    |||| |  |   || ||        |  | | |        ||| || | | ||||  ||||||   |                      
GGCTTTGAATGAAATTTATGCTGAGGAAGAAGACTATGACAGACTCCGTGAATCAATAGATCTGCATGATAACTTCGATCAGATAGGTCTTGCACAGAAGgtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 24

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaa------ataaaaataaaatagccaga-cagtcgtgcaattcctatcg------ctaccgct--tttaatttaataacatgtgttaatttattgagcag
||| ||||||||| ||||||| || || |||||||| || ||||| | ||||||| | ||  ||||||||||||| || ||||| |||||||| |||||||| ||       ||    | |||| || | |   |   |   | || ||  |       ||  | |  |||  ||| |  | |||| ||  ||| ||      
AGCTTTGAATGAAATTTATGTTGAGGAGGAGGACTATGATAGACTTCATGAATCAATAGATCTGCATGACAACTTCGATCAGATAGGTCTTGCACAGAAGgtgaatcttccgtatctttcaaattgctaaaattgaaatctgaatcttactgagaaacttaggggtcatttggtttgaagaaatgtttttttttttttct---

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 26

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaa------taaaaataaaatagccaga-cagtcgtgcaattcctatcgctaccgctt--ttaatttaataacatgtgttaatttattgagcag----
||| ||||||||| ||||||| || || |||||||| || ||||| | ||||||| | ||  ||||||||||||| || ||||| |||||||| |||||||| ||       ||    | |||| || | |   |   |   | || || ||  ||   |   |   |||  |      | || ||||  ||         
AGCTTTGAATGAAATTTATGTTGAGGAGGAGGACTATGATAGACTTCATGAATCAATAGATCTGCATGACAACTTCGATCAGATAGGTCTTGCACAGAAGgtgaatcttccttatctttcaaattgctaaaattgaaatctgaatcttaccgagacatttgggtgtgtttggtt-tgcattttcattttctgttttcattt

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 26

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaat-------agccagacagtcgtgcaattcctatcgctaccgcttttaatttaat-aacatgtgttaatt--tattgagcag--------------------
||| ||||||||| ||||||| || || || |||||||| |||||||| |||||| | ||  |||||||||||||||| ||||| |||||||| |||||||| ||       ||   |       |    |||| |     || ||  |   |      || |     | | || |||| | ||||  ||||||   |                    
AGCTTTGAATGAAATTTATGTTGAGGAAGAAGACTACGACAGACTCCGAGAATCAATAGATTTGCATGACAACTTTGATCAGATAGGTCTTGCACAGAAGgtgaatctcggttatcttttgtcttattttgacaattagcaaaatctgagatcaggaagttatggaaaatttaaaatgtttgaattattattgattggcttcaacaatacatgagcag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 26

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatagccagacagtcgtgcaattcct----------atcgctaccgcttttaatttaataacatgtgttaatttattgagcag----
 ||  |||||||  | || || ||||| || |||||||| ||  | || || ||  ||||  | ||||||| ||||||||||||||| || || ||||||||||| |  ||||| | || ||    | |  |     || |          |     |  || ||  |  | |||  || |     |  || | ||      
GGCTCTGAATGAGATATACGTGGAAGAAGAAGACTACGATAGGTTGCGAGAGTCTATTGATTTACATGACAGCTTTGACCAGATTGGCCTCGCTCAGAAGgtaaagttcaaatatactacccctttaatattttctctctttaaaaatggaaaaagaatggccttagagatgatataatcttcctgtgaatggtgcgaacag

upper sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 26

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaaaataaaatagccagacagtcgtg-caattcctatcgctaccgcttttaatttaataacatgtgttaatttat-tgagcag
||| || ||||   || |||| || || |||||||| || ||||| || |||||| | || |||||||| |||||||||||||| || ||||| |||||||| | | | |   ||  ||    |  | |  ||  |      ||    |   | | ||     |||| || |  | ||   | ||  |||
AGCATTAAATGGTATTCATGTAGAGGAGGAGGACTATGATAGACTTCGGGAATCAATAGATATGCATGATAACTTTGACCAGATAGGCCTTGCACAGAAGgtgagagagattgaatttattttgttaatgttggtaggcttcataagcagaacatgtac----ataagatctagtgatgcgtgtggacag

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|26455954|gb|CA827537.1|CA827537

EST:     AATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG                         CTTGAGAAGCATGAAATGCTGGAGATGAGGAGGATCGCCGCCTACATTTAC
genomic: AATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaa ... tattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTAC

EST: gi|19770178|gb|BQ034899.1|BQ034899

EST:     AATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG                         C-TGAGAAGCATGAAATGCTGGAGATGAGGAGGATCGCCGCCTACATTTAC
genomic: AATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaa ... tattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTAC

EST: gi|211415581|gb|FL028985.1|FL028985

EST:     CATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG                         CTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTAC
genomic: CATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaa ... tattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTAC

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: 451

AGCCTTGAATGAACTTTATGTCGAAGATGAGGACTACGAGAGACTCCGTGAATCAGTTGACATGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAGgtaaaataaa ... tattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCCATTGCTCTATCGAAGAAAGACA

Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 284

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357