ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtgggtggtttctcccctttcctgctctaacttatctgcaaattgttatcatgtaccttatgagtgaacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC

Basic information

species	Zea mays
transcript	GRMZM2G119773_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g56970.2 (Oryza sativa), 3'ss of exon 4

gtgggtggtttctcccctttcctgctctaacttatctgcaaattgttatcatgta--ccttatgagtgaacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC
    ||   |  ||  |||  ||   ||       ||| || |||| ||||   |   || ||  |  ||| ||||||||||| ||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||| ||||| ||||||||||||||||||||||||||||
----gtaagtattcttcttatctatgctg------ctgtaacttgtgatcacacaatactcatctgaaaactttgcagATACCTGGACTTGTCAATGTTGATTTTGCTGATGTGAAAGCTGTTATGAAAAACTCTGGAACTGCAATGCTTGGTGTTGGTGTTTCTTCCAGCAAAAATC

upper sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 5

-----gtgggtggtttctcccctttcctgctctaacttatctgcaaattgttatcatgt-accttatgagtgaaca------------------ttgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC
     | | || | | |||| |  |  |     || | ||    |     || | |||| | ||| ||||   |                    || |||||||| || ||||| ||||| ||||||||||||||||||||||| |||||| ||||||||||||| ||||| ||||| |||||||| ||||| ||||| |
tatttgagtgttgctcctccaccataattggacaattaatgaaaagtacattttgatgtcagcttttgaggatattatttgctgttgcatctttttacagATACCCGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCTATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC

upper sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 5

-------------------------gtgggtggtttctcccctttcctgctctaacttatctg--caaattgttatcatgtaccttatgagtgaacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC
                          |||    ||  |      | |   |  |  | | ||   ||   ||||||   ||      ||  |     || |||||||| || ||||| ||||| ||||||||||||||||||||||| |||||| ||||||||||||| ||||| ||||| |||||||| ||||| ||||| |
tttcagtgttgctcctccatcataattggacaattaatgtaaagtacattttgatgtcagcttatcaggatgttattcagtgttacgtgtct---ttttacagATACCTGGGCTTGTAAATGTGGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGAACTGCAATGCTTGGTGTGGGTGTTTCCTCCAGTAAAAACC

upper sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 4

--------------gtgggtggttt--ctcccctttcctgctctaact-tatctgcaaattgttatcatgtaccttatgagtgaacat-------tgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC
               ||||   |||  ||   | ||| ||       | | ||      || || |  |  || |||| |       |       ||||| |||| |||||||||||||| |||||||| |||||||||||||| |||||| ||||||| ||||| ||||| || || |||||||| ||| | ||||| |
tcacttcttcataattgggcattttggctttgcattcatgtcaagggtatgtccatgctttttttttctcgacattataaactgttgtgccttcttgcagGTACCTGGACTTGTCAATGTGGATTTTGCAGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGAGTAGGTGTTTCCTCCGGTAAAAACC

upper sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 4

-----------------gtgggtggtttctcccctttcctgctctaact-tatctgcaaattgttatc---atgtaccttatgagtgaacatt---gcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC
                 | |  | ||  ||   | ||  ||       | | ||     ||| || ||   |   |    |   |||  | ||   |||| |||| |||||||||||||| ||||||||||||||||||||||| |||||| ||||||| ||||| ||||| ||||| |||||||| ||| | ||||| |
acttctccttcataattgggcattgtggctttgcatttatgtcaagggtatgtccatggatttttttctcaacacagtaaactggtgtgccttcttgcagGTACCTGGACTTGTCAATGTAGATTTTGCTGATGTAAAAGCTGTGATGAAAGACTCTGGGACTGCAATGCTTGGTGTAGGTGTTTCATCCGGTAAAAACC

upper sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 4

--------------------------gtgggtggtttctcccctttcctgctctaacttatctgcaaa--ttgttatcatgtaccttatgagtgaacattg--cagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC
                           |     |||  |              | | | |||  ||||  || | |  |   |   |||   |     ||   |||||||| ||||| |||||||| |||||||| ||||| || || ||||||||| | ||||||||||| |||||||| || |||||||||||||||||||| |
gtgagtctatgtattgtataaagcacataacaagttggttgatgaatgcttattgattgatccccaaagattctgaggaaacagtatatattttgttctttttcagATACCTGGACTAGTCAATGTAGATTTTGCAGATGTGAAGGCAGTCATGAAAGATTCTGGAACTGCAATGCTCGGGGTAGGTGTTTCTTCCAGCAAAAACC

upper sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 4

------------------gtgggtggtttctcccctttcctgc--tctaacttatctgcaaattgt-tatcatgtacctta---tgagtgaacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC
                   |   || ||  |  ||  | |||   | || |||  |||   ||  | ||| || ||   ||   ||        ||||||||||| || || || |||||||||||||| |||||||| || ||||||||  ||||||||||||| ||||| || || || ||||||||||||||||| |
actgatttattatgatattttcctgattaatttccaatactgaagtttatctttgctgttgatcctatataatttaaaatagcgtgtccttgttttgcagATACCCGGGCTGGTAAATGTTGATTTTGCAGATGTAAAGGCAGTCATGAAGGACTCTGGAACTGCAATGCTTGGAGTGGGGGTTTCTTCCAGCAAAAACC

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|148970650|gb|EE021357.2|EE021357

EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCAT
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCAT

EST: gi|148940468|gb|EC885267.2|EC885267

EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA

EST: gi|211174836|gb|FL413961.1|FL413961

EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAA

EST: gi|76923027|gb|DV169298.1|DV169298

EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA

EST: gi|211392485|gb|FL384044.1|FL384044

EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA

EST: gi|148941071|gb|EC885931.2|EC885931

EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTT
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTT

EST: gi|149097959|gb|EE183902.2|EE183902

EST:     AGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCANCA                         -TACCGGGACTTTGTCA-TGTTGATTTTGCTGATGTAAAAGCTGTCATGA
genomic: AGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCA-CAgtgggtggtt ... aacattgcagATACCGGGACTT-GTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGA

EST: gi|149097351|gb|EE183189.2|EE183189

EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA

EST: gi|60356845|gb|DN223818.1|DN223818

EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA

EST: gi|78078489|gb|DV506902.1|DV506902

EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA

EST: gi|211478791|gb|FL377823.1|FL377823

EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA

EST: gi|148971012|gb|EE021841.2|EE021841

EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCCNATGT-GATTTTGCTGATGTAAAAGCTGTCATGAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCA-ATGTTGATTTTGCTGATGTAAAAGCTGTCATGAA

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), 48 (downstream exon)
Score: 263

ATTAGATGTTGCGGATGAAAACATGCCCTTGCAAGATGCATTTCTCCTTGCAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 131

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 86

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 123

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctgctctaacttatctgcaaattgttatcatgtaccttatgagtgaacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC