ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcag

Basic information

species	Zea mays
transcript	GRMZM2G063949_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 5

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcag
 ||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||| ||||| |||||||||||||| || |||||||||||| ||   |  ||  |||  |||| || ||   | |    ||||   |   ||| ||  | |||||| |||||| | |   ||||||  |||||||
TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaaccagtccctttctgagaataatatacct--ccattt---cgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 5

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcag--------
 || || || || || |||||||||||  | ||||| |||||||||||  |||||||||| ||||| ||||| ||||||||| | |||||||| || || || ||| | |||  || ||| |   | |  || |   | ||  ||    |   |   | |  || | | ||  ||  |        || |||             
TGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGAGGGTGTTCCTCGGGTTCTTGCTTGCTTTAGCAATgtcagt-tacttactt-ttgctattgctttttgttgaagtttgttg-atattttagccggagttttgaaaatttgttcaaattttctgttttcctttgtctgcag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA12G30490.2 (Glycine max), 5'ss of exon 5

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcag--------------
 ||||| ||||| ||||||||||||||| | ||||| |||||||| ||  ||||||| || ||||| ||||| ||||||||| |||| ||||| || || || |||    ||   | ||| |   ||   ||   ||||   | |||  |   |  ||  | || |  ||  |||     |   |||  |||  |                
TGTGAGGCCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGCCCAAGTGAGGGTGTTCCTCGGGTTCTGGCATGCTTTAGCAATgtgagt----ttacattttgatttagac--tttgtttaagcttgtatatatgttactcgatatttttggataatg---attctaaatattttctccattccttttctgtag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA17G05440.1 (Glycine max), 5'ss of exon 3

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtct-tctcagaagatgcacggtaccaatggttttgcag---------------
 ||||||||||| ||||||||||||||| | ||||| |||||||| ||  |||||||||| ||||| ||||| ||||||||| |||| ||||| || || || |||    ||   | ||| |   ||   ||   ||||   | |||  |   |  | ||||  | |    | ||  | | | | ||   ||||                   
TGTGAGACCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGTCCAAGTGAGGGTGTTCCTCGGGTTCTGGCATGCTTTAGCAATgtgagt----ttacattttgatttagac--tttgtttaagcttgtatatattgttgttagtcaatatttttaaata-atgattctaaatattttcttcatttcttttctgtag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 5

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgc-accatgttcagtcttctcagaagatgcacggtaccaatggttttgcag
 ||||| ||||| || |||||||||||  | ||||| |||||||||||  |||||||||| ||||| ||||| ||||||||| | || ||||| || || || ||| | |||  || ||| |  |    | | | |  || ||||  || |   | || |   ||     || ||   | ||     |   | |||||
TGTGAGGCCTTTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGCATTGATGGTCCAAGTGAGGGTGTTCCTCGGGTTCTTGCATGCTTTAGCAATgtcagt-tacttactt-ttgctatgttgaagtttttagatgattttagccagagttttgaaaatttgttcaaaattttctgttttcctttgtctgcag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 5

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcag
|||  ||||||| || ||||||||||| |||||||| ||||| || ||  ||||||||||||| |||||||| || || ||  | || ||||| ||||||||||||||||   |  |   ||    | |   ||  || |    | || |  || | ||  ||| | ||   |||||     | |    | || |||
CGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGAAGGTGTCCCACGTGTCCTTGCCTGCTTTAGTAACgtaagtgttcaaat--ccaagtatataacccaatgctagt---ctgtgtat-atatgcaagctt-ttagttaatgcat--ctctatctatctttcag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 5

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcag
 || ||||| ||||| ||||||||||| |||||||| ||||| |||||  ||||||||||||| || ||||| || |||||| | || ||||| |||||||||||| | |  | ||  |    | || |    |  |  | ||   |||| |   || | | || |    |  |    |||     |  |||     
TGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGAGGGTGTCCCACGGGTTCTAGCGTGCTTTAGTAACgtaagtatacaggcttagtc-caatgacctgagttcttctcatggctgcagc---ttaacttttttgtttaactttttggtg--ggtattttcag--

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 5

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcag
 ||||| ||||| || |||||||| || || ||||| |||||||||||  |||||||||||||||||||||| ||  ||||| |||| |||||||| || || ||| |     | | |     |  ||   |   ||  |  | | |    ||| ||   |  |||| ||   ||| |  |  |  |      | ||
TGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGAAGGTGTTCCAAGGGTTCTGGCATGCTTCAGCAATgttagtttcaacatctgtca--taacatggcttgtttggtagtatttttttcatttttt-ttgtctctgatcttgctctttttc--tcccaccgtag

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|22715502|gb|BU197799.1|BU197799

EST:     TTGATGGTCCTAGTGAAGGTCTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|109637685|gb|EC591230.1|EC591230

EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTNTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAAAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|149086197|gb|EE175737.2|EE175737

EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|6021071|gb|AW065999.1|AW065999

EST:     TGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGNTGATGGGGGTCAGTCTCAG
genomic: TGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTT-GGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|40337281|gb|CK371351.1|CK371351

EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|60356652|gb|DN223625.1|DN223625

EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|32868566|gb|CF008248.1|CF008248

EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|67020590|gb|CO449339.1|CO449339

EST:     TGATGGTCCCTAGTGAAG-TGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAA
genomic: TGATGGTCC-TAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|67011006|gb|CO439755.1|CO439755

EST:     GATGGTCCTAGTGAAGGTGTGCCCCTCGG-TTT-GGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: GATGGTCCTAGTGAAGGTGTGCC--TCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|149086196|gb|EE175736.2|EE175736

EST:     GGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: GGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|31356398|gb|CD440755.1|CD440755

EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|7137694|gb|AW499223.1|AW499223

EST:     TTGATGGTCCTAGTGAAGGTCTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|31355714|gb|CD440071.1|CD440071

EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

EST: gi|211213926|gb|FL245933.1|FL245933

EST:     TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAAC                         AATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG
genomic: TTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAG

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: 304

CGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGAAGGTGTGCCTCGGGTTTTGGCTTGCTTCAGTAACgtaagtgttc ... ggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 89

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 34