ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaactaatcttgtgctaaaagaaacatgtatgatacagctactatatgatagtgagttctctttctactggttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCC

Basic information

species	Zea mays
transcript	GRMZM2G001457_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G001457_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g01140.3 (Oryza sativa), 3'ss of exon 20

-------------------------------------------------------------------------------------------------------------------gtaactaatcttg--tgctaaaagaaacatgtatgatacagctac---tatatgatagtgagttctctttctactggttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCC
                                                                                                                    || |  ||| ||  || | | |  |   | |  || |  | ||    |||  | | ||| ||  |   |||| | ||||  ||||| |||||||||||||| ||||| |||||||||||||| || ||||| ||||| || ||| ||||||||||||||||  ||||||||||||||||||||||
gtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttatgaggtggtg-gtaatgaatctatttgttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCC

upper sequence: GRMZM2G001457_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g01140.1 (Oryza sativa), 3'ss of exon 20

-------------------------------------------------------------------------------------------------------------------gtaactaatcttg--tgctaaaagaaacatgtatgatacagctac---tatatgatagtgagttctctttctactggttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCC
                                                                                                                    || |  ||| ||  || | | |  |   | |  || |  | ||    ||   | | ||| ||  |   |||| | ||||  ||||| |||||||||||||| ||||| |||||||||||||| || ||||| ||||| || ||| ||||||||||||||||  ||||||||||||||||||||||
gtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttacgaggtggtg-gtaatgaatctatttgttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCC

upper sequence: GRMZM2G001457_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 21

-------------gtaact-aatcttgtgctaaaagaaacatgtatgatacagctactatatgatagtgagttctctttctac------tggttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCC
             | |||| || ||  || |       ||||  | || ||| |   || |  | |     | || |  || |      |  || | |||||||||||| ||||||| ||||| ||||| |||||||| ||||| || || || || ||||| |||||| | |||||||| ||||||||  | | ||||||
gaatttaatggccgaaacttaacctattggtctctttcacataaaagacaca-cggatacactaaaaaacatactttgactgcatgccttacttttttcagGAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGACTAGGCAAAGAACATTTACAAATATTCTCCACAAGGACCTTAAATTTCC

upper sequence: GRMZM2G001457_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G40550.1 (Glycine max), 3'ss of exon 19

-------------------gtaactaatcttgtgctaaaagaaacatgtatgatacagctactatatgatagtgagttctctttctactggttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCC
                     |   ||   |   ||   |  || || |   | | |   |   |||   |    | |    ||| |    || | | ||| |||||  ||||||| ||| | ||||| ||||| || ||| | ||||||||||||||||  |||||||| |||||||| ||||||||  | | ||||||
ctgtcggactttttcacatacacaaaaggcttcactcggatgaatatttggaacaaattaaaattatatcacattgcttgacttcaatgactttttttagGTATTCTAATATATGAAATGCTTTATGGGTATACGCCATTCCGGGGGAAAACAAGACAAAAAACATTTGCAAATATTCTTCACAAGGACCTTAAATTTCC

upper sequence: GRMZM2G001457_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 20

---------------------gtaactaatct-tgtgctaaaagaaacatgtatgatacagctactatatgatagtgagttctctttctactggttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCC
                     ||      | | ||  ||||||     |  | | |  ||  |||| | |  |      ||   | | |  | | | | | ||| |||||||||||||| ||| | ||||| |||||||| || || || || ||||| |||| ||||||||| || ||||| ||||| ||| | | ||||||
aaatactatatatgtgtgtgtgtgttccctttgtgcactaaaactcttaattttaactcaa-tactgttt--tttctgattgattatatgtttgctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCC

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|6672132|gb|AW282307.1|AW282307

EST:     TGTAGATTGGTGGGCGCTAG                         GGGTTCTTCTATATGAGATGTTATATGGTTATACACCCTTCAGAGGGAAAA
genomic: TGTAGATTGGTGGGCGCTAGgtaactaatc ... gttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAA

EST: gi|28985222|gb|BQ538375.2|BQ538375

EST:     CTGGCCATACGAGTGCTGTAGATTGGTGGGCGCTAG                         GAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAA
genomic: CTGGCCATACGAGTGCTGTAGATTGGTGGGCGCTAGgtaactaatc ... gttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAA

EST: gi|18164960|gb|BM334799.1|BM334799

EST:     GATTATTACCGGAGCTGGCCATACGAGTGCTGTAGATTGGTGGGCGCTAG                         GAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAA
genomic: GATTATTACCGGAGCTGGCCATACGAGTGCTGTAGATTGGTGGGCGCTAGgtaactaatc ... gttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAA

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: 26

ATAGTCATCATCTGTTTTATCAATCCTTGTATTGTATGCATGCTGTAGGAGATTATTACCGGAGCTGGCCATACGAGTGCTGTAGATTGGTGGGCGCTAGgtaactaatc ... gttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 365

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 99

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atgtatgatacagctactatatgatagtgagttctctttctactggttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCC