ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

Basic information

species	Zea mays
transcript	GRMZM2G124886_T04
intron #	13
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 13

gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaa---aacatgtttctttgt--gtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
|| |   | |||||| |   |||     |||  ||||||| | |    | |||||| ||| || ||   || ||    |  || ||  || |  ||||||||| || ||||| || |||||||||||||| |||||||||||||| || ||||||||||||||||| || |||
gtgagtaattttgttcctggatt----taaatttttttttgcgt----gtcatttggaatattatgatgctaaataggatctgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 4

gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaa-----catgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
|| |   | ||||||     ||   ||||||  | ||||      | || |||||| ||| || ||   || || |     |   ||  | | |||||||||| || ||||| || |||||||||||||| |||||||||||||| || ||||||||||||||||| || |||
gtgagtaattttgtt----catggattcaaatttattttg-----cgtgtcatttggaatattatgatgctaaataggatccgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13

gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
|||| | | |||| |    |   |||| |    | |  |    | | |   |||     | |  |   | |       |  |  | |||  |||| || ||||||||||||||||||||| ||||||||||||| || ||||| |||||||||||| |||| || |||
gtaa-gtactttgattaggtgacattt-agttatctgctcttttccttcttattcattgtttaatataattttgttattaatcttgtgt-cagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2

gtaatggaatttgttacct--tattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgt-agAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
||||  |  |   | |  |   || |  |     ||||| || | ||| | |  |||    ||||       | ||||    |||  |||||| |||| || ||||||||||| ||||||||| |||| || ||||| |||||||| |||||||| ||  |||| || |||
gtaagtgcttgcatgaggtgacatcagctttctgcttttatttc-ttcttactgtttct--tgttaattttgttaaaa----ttttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 13

gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
     | || |  || | | |    |   | |   ||| | | || ||  | | | |    || |     |    | || ||||||     |||| || ||||||||||| || ||||||||||| || ||||| |||||||| |||||||| ||  | || || |||
-----gtaagtgcttgcatga--ggtggcatcagctttctgcttttatttcttcttactgtttcttatttttgttaaatttttcttgtgtcagAACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 13

gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaat-gttgtgccactcaaaaca--tgtttct-ttgtgt-agAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
         |  ||    | ||||  | | | ||  || |    || |  | ||   | | |||||   | | ||      | ||| | |||||| |||| || ||||||||||||||||||||| ||||||||||||| |||||||| |||||||||||| |||| || |||
--------gtaagtactttgattaggtgacatctagttatctgctcttttccttcttattcgttgtttaatttaattttgttatttatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17

--------------------------------------------------------------------------------------------gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgta--------gAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                                                                                              ||  || ||  ||| || |  | || ||||        | |||  | |   | |     || |  ||||   ||| | ||| ||| |  |        ||||||||| ||||| |||||||||||| ||||  ||||||| |||||||| |||||||||||  | || |  |||
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctga--aatttaaacgcaaaagcagattggtactgctcgc----ttat-tcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13

-----------------------------------------------------------gtaatggaatttgttacctta----ttatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                                                            || |||||  |  || | |     | | ||  |   |||  |    |   |    | | |  ||| |||   ||    ||||     ||   | ||||||| || |||||||||||||||||||||||| | ||||| ||||| || ||||||||||| |||||||  || 
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgct----acataacgttt---gcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13

---------------------gtaatg-gaatttg----ttaccttattatttcaaacctttttttacattca--tgccatttgaaatgttgtgccactcaaaacatgt-----ttctttg---------------tgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
                     ||  || ||| ||     | | |   || || |||  || |  |||||||    |  || |||||| ||||| ||| | |     | |      |||||                || |||||||||| |||||||| ||||||||||||||| | ||||| |||||||||||||||||||| ||||| || |||
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaa-gttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13

----gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT
    ||  |  ||    |||| | |  ||| | |   |||    |||   |  | |      ||  |      ||         ||   |  |  |||||||||| |||||||| ||||||||||||||  |||||||||||||| | ||||| ||||| || || || |||
gcatgttctcaaaaagcttacttcacaattaccaggttttggccacagagaaacta------atagttcatttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT

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|31355222|gb|CD439579.1|CD439579

EST:     ATGATTGGGTGGAATGCAGATTGATACGCCGAATTGATGTCAATGTGAAG                         AATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACG
genomic: ATGATTGGGTGGAATGCAGATTGATACGTCGAATTGATGTCAATGTGAAGgtaatggaat ... ctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACG

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: 170

ATTTGGTGGTGTGTTACTTGCTATGTGTACAAATGACTTCATTTGCTTTTATGATTGGGTGGAATGCAGATTGATACGTCGAATTGATGTCAATGTGAAGgtaatggaat ... ctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 266

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 239

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT