ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtatagtgtaccatgattgagagcacatgaattgatattcagtaagaaaattcacctattggctgctattaaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG

Basic information

species	Zea mays
transcript	GRMZM2G069008_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G069008_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g03910.1 (Oryza sativa), 3'ss of exon 3

-----gtatagtgtaccatgattgagagcacatgaattgatattcagtaagaaaattcacctattggctgctattaaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG
      |||  |     |   |  |  || |||    || |||| || |       |    ||| | | ||| | |||| | ||||||||||||||| ||||||||||  | ||||| || ||||||||||||||||| || ||||| || |||||||||||||| ||||||||||||
gtatgttatcatcagttactgtgaatggctcatattctggtatt-agaaccttgtgttgagtatcgaccgctctgaaaattttagGTTAGAGTTCCTGTTGGAAAATTTATATTGGAACTACCTGCTGGGATGCTAGACGATGAAAAGGGAGATTTTGTTGGCACTGCAGTCCGTGAG

upper sequence: GRMZM2G069008_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G04160.1 (Glycine max), 3'ss of exon 4

------------gtatagtgtaccatgattgagagcacatgaatt--------gatattcagt--aagaaaattcacctattggctgctattaaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG
            |  | ||||    |  ||  ||| |  |  |||        ||| |||| |  | |   ||||   | |||| |  | |||    |  |||  || |||||| |||||| |  | | |||||  |||||||||| ||| | ||||| || ||||||||||||||||| || ||||| ||||||
gtagacactggtgccttgtgttttttttttttgagaaattatatttttaactggattttcattttatggctattcttatgttggttattcttatttata-agGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTGCGTGAG

upper sequence: GRMZM2G069008_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G04150.1 (Glycine max), 3'ss of exon 4

--------------------gtatagtgtaccatgattgagagcacatgaattgatattcag--taagaaaattcacctattggctgctattaaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG
                    || |  | |    | ||| | |    || | | ||| ||||   || |   |||    | |||| |  | |||    |  |||  || |||||| |||||| | |  | |||||  |||||||||| ||| | ||||| || ||||||||||||||||| || ||||| ||||||
gtagatgctggtgccttgctgtttttttttatttaatt-atattttataactggattttcatgttatggctattgttatgttggatattcttatttgta-agGCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTTCGTGAG

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|78087423|gb|DV515816.1|DV515816

EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

EST: gi|148991429|gb|EE032931.2|EE032931

EST:     GAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: GAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

EST: gi|45847993|gb|CN071936.1|CN071936

EST:     ACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: ACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

EST: gi|149074764|gb|EE163194.2|EE163194

EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

EST: gi|148942502|gb|EC887517.2|EC887517

EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

EST: gi|91054277|gb|EB164695.1|EB164695

EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

EST: gi|29544119|gb|CB604499.1|CB604499

EST:     AGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: AGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

EST: gi|149096585|gb|EE182343.2|EE182343

EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

EST: gi|149111714|gb|EE190861.2|EE190861

EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

EST: gi|78082236|gb|DV510648.1|DV510648

EST:     TGGAGTCGAATGGAGAAACATATGCTGTGCTTTCCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

EST: gi|113703128|gb|EE680632.1|EE680632

EST:     TTGGGGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

EST: gi|29543762|gb|CB604142.1|CB604142

EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

EST: gi|31355362|gb|CD439719.1|CD439719

EST:     TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAG                         GTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA
genomic: TGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTA

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: 48 (upstream exon), 49 (downstream exon)
Score: 49

GTTCCAGGAATTGTCTTTGCAAGAGGGCCCGCGGTTGCTGTGTTGATTCTTTTGGAGTCGAATGGAGAAACATATGCTGTGCTTACCGAACAGgtatagtgta ... aaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 72

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 57

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 81

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

catgaattgatattcagtaagaaaattcacctattggctgctattaaaactgtagGTTAGAGTTCCTATTGGAAAATTCCTGTTGGAGCTGCCTGCTGGGATGCTAGATGACGAAAAAGGTGATTTTGTTGGCACCGCAGTCCGTGAG