ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtttttaaaaactacaaaataatgcctctatgtactcgaatttctggttttcattcgtccttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAG

Basic information

species	Zea mays
transcript	GRMZM2G000749_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 3

----------------------------gtttttaaaaactacaaaataat-gcctctatgtactcgaatttctggtt--ttcattcgtccttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAG
                              |||||   |    ||| |  |   |  | || |||| |||||||| ||  ||  ||  | ||||  |||| ||||||||||||| || ||||||||||| ||||||||||| ||||| |||||||| ||||| ||||||||||||||||||||||||
gtttcttctgcgttctccaattgtttatcattttattgaggggaaattgtttatcattgtgaactcaaatttctgtttacttggtttcttcttgtgcaaaaagGTAATGCATGGGGCTGATCGTGATATTATGTGGCTCCAACGGGATTTCCACATATATGTTTGCAATCTTTTTGACACAGGACAG

upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 3

-gtttttaaaaactacaaaataatgcctctatgta----ctcgaattt--ctggt----tttcattcgtccttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAG
  ||| |  | | | |  |||      ||||   |    || |||| |   |  |    | | |  |    |   | || |||||||| ||||| || ||||| ||||| || ||||| || ||||||||   ||| ||||| ||||||||||||||||||||||||
gttttctccataatgcgcaatgtgttttctacagaattcctagaatatagttaatacaatatgaaaccatttaacttaactagGTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAG

upper sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 3

gttttt----aaaaactacaaaataatgcctctatgt----actcgaatttctg-gttttcattcgtccttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAG
||||||      | ||| |||    ||  |   | ||    | |  | |||||| | | | |    |  ||    || |||||||||||||| || ||||| ||||| || ||||| || |||||||||  ||| ||||| |||||||| |||||||||||||||
gtttttcctgggatacttcaattccattacaaaaggtctaaaatatattttctgtgctctgaaatctgtttatgtaattagGTAATGCATGGAGCAGATCGAGATATTATCTGGCTTCAACGGGACTTCGGCATATATGTCTGCAATCTCTTTGACACAGGACAG

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|211268121|gb|FL015554.1|FL015554

EST:     ACATTGGTCTCTATTTGCAAGAGCCTTTCAAAGATCCAACAAAGAGAAAG                         GTAATGCATGGTGCGGATCG
genomic: ACATTGGTCTCTATTTGCAAGAGCCTTTCAAAGATCCAACAAAGAGAAAGgtttttaaaa ... ggtcaaatagGTAATGCATGGTGCGGATCG

EST: gi|60338799|gb|DN205772.1|DN205772

EST:     ACATTGGTCTCTATTTGCAAGAGCCTTTCAAAGATCCAACAAAGAGAAAG                         GTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCAC
genomic: ACATTGGTCTCTATTTGCAAGAGCCTTTCAAAGATCCAACAAAGAGAAAGgtttttaaaa ... ggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCAC

EST: gi|211270566|gb|FL015574.1|FL015574

EST:     CATTGGTCTCTATTTGCAAGAGCCTTTCAAAGATCCAACAAAGAGAAAAG                         GTAATGCATGGTGCGG
genomic: CATTGGTCTCTATTTGCAAGAGCCTTTCAAAGATCCAACAAAGAGAAA-Ggtttttaaaa ... ggtcaaatagGTAATGCATGGTGCGG

EST: gi|211270560|gb|FL015568.1|FL015568

EST:     ACATTGGTCTCTATTTGCAAGAGCCTTTCAAAGATCCAACAAAGAGAAAG                         GTAATGCATGGTGCGGATCGTGATAT
genomic: ACATTGGTCTCTATTTGCAAGAGCCTTTCAAAGATCCAACAAAGAGAAAGgtttttaaaa ... ggtcaaatagGTAATGCATGGTGCGGATCGTGATAT

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: 46 (upstream exon), 44 (downstream exon)
Score: 86

TTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGCTACGCATATACATTGGTCTCTATTTGCAAGAGCCTTTCAAAGATCCAACAAAGAGAAAGgtttttaaaa ... ggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAG

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 133

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aataatgcctctatgtactcgaatttctggttttcattcgtccttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAG