ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CAGGAAGGCAACACTGTGCATTCATCCTGATAAGGTGCAACAGAAAGGTGCAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaacgtgatcaacttatttggcaacgtttaatatgataaatgagacaggtagaaattcattttttaggagacacatactaattgtgacaccgta...

Basic information

species	Zea mays
transcript	GRMZM2G158872_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G158872_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g43950.1 (Oryza sativa), 5'ss of exon 7

CAGGAAGGCAACACTGTGCATTCATCCTGATAAGGTGCAACAGAAAGGTGCAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaacgtgatcaacttatt-tggcaacgtttaatatgataaatgagacaggtagaaattcattttttaggagacacatactaattgtgacaccgta------
||| ||||||||| | ||||| |||||||| |||||||||||||| |||||||  |||||||||||||||| ||| || || || ||||| |||||||||||  ||  |    ||||    ||     |||   || | |||  | |||| ||    |  | ||||      || |||   ||  | ||||  |||| |        
CAGAAAGGCAACATTATGCATCCATCCTGACAAGGTGCAACAGAAGGGTGCAAATCTTCAGCAGAAATATACTGCAGAGAAGGTGTTTGATATTCTTAAGgtgtgt--atagtatcactgcatcgcaacaaatattgaaatgccatatgaaactt-caatatttcacgc---agaagaactatcattattgc-acactggcaactag

upper sequence: GRMZM2G158872_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT4G12780.1 (Arabidopsis thaliana), 5'ss of exon 7

CAGGAAGGCAACACTGTGCATTCATCCTGATAAGGTGCAACAGAAAGGTGCAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaacgtgatcaacttatttggca-------acgtttaatatgataaatgagacaggtagaaa--ttcattttttaggagacacatactaattgtgacaccgta----------------------------------------
||||||||| || || || || || |||||||| || || || ||||| || |  || ||||||||||| |||||||| ||||| |||||||| || |||||| |||||  | | ||  ||  | |  |       |    |  ||    |  ||  || |  | ||    |    ||||| ||   ||     ||||||   |    |                                        
CAGGAAGGCCACTCTATGTATACACCCTGATAAAGTTCAGCAAAAAGGAGCCAATCTCCAGCAGAAATACATTGCCGAGAAAGTTTTTGACATGCTCAAGgtaagtgaat-tcaccatttttctggaaataaatccatcactgctacttcagctgccaccgacaaaacaccttgcattttacgaataactgcacaattgtataaatccacatttgctggcttaatctcctttgtcatgacaataaacag

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|6227229|gb|AW155828.1|AW155828

EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAN                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCC
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCC

EST: gi|32863076|gb|CF002758.1|CF002758

EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT

EST: gi|5847361|gb|AW000440.1|AW000440

EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT

EST: gi|5860429|gb|AW011651.1|AW011651

EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACC
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACC

EST: gi|5325205|gb|AI783396.1|AI783396

EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCC
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCC

EST: gi|116816443|gb|EC859181.1|EC859181

EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT

EST: gi|32836578|gb|CD976256.1|CD976256

EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT

EST: gi|5895879|gb|AW037125.1|AW037125

EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGN
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT

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: 76

CAGGAAGGCAACACTGTGCATTCATCCTGATAAGGTGCAACAGAAAGGTGCAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGTGACTGTGAATATGCATATATGATGGACAGCTTAACTGCATACCAACATG

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 87

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147