ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...gaatcaactgcccgcccagtgttaccacctgtgcttaacatggaaaatgcatctgtcggttaccaacaaaaggtgtctaacatattcaagctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCAGCATATGCATTTAGATTTGTGGGTGACTGGCTGAAGTGGCTATACATGG

Basic information

species	Zea mays
transcript	GRMZM5G864319_T01
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 7

gaatcaactgcccgcccagtgtt-accacctgtgcttaacatggaaaatg----catctgtcggttaccaacaaaaggtgtctaacatattcaagctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCAGCATATGCATTTAGATTTGTGGGTGACTGGCTGAAGTGGCTATACATGG
   | || |    |  |  |||| | |        ||||  ||  ||| |     | || |  | ||||||  | | ||| ||||    |  |   ||||||||||||||  ||||||||||||| ||||||||||||||||| |||||||||||||| ||||||||||| ||||||||||| |||||||||||||| |||| ||
---ttaa-tatttgtactttgttcatctaaaagaattaaattgataaacgagtttaactttttgctaccaatgacaagtggctaatg-gtctataatggttacagGTCCTCAATTACAAGACTCAGCAAAGCAGACTCTTTCCTTTGCTGGCTTCAGCTTATGCATTTAGGTTTGTGGGTGAGTGGCTGAAGTGGCTGTACACGG

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA11G03800.1 (Glycine max), 3'ss of exon 7

----------------------------------------------------------gaatcaactgcccgcccagtgttaccacctgtgcttaacatggaaaatgcatct---gtcggttaccaacaaaaggtgtctaacatatt---caagctggttac-------agGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCAGCATATGCATTTAGATTTGTGGGTGACTGGCTGAAGTGGCTATACATGG
                                                             | || |        ||   ||    |||   | || ||  ||||||    |    |  ||| |   | ||  ||      | ||||   |    | | |         ||||  |||||||||| || || ||    || ||||| || ||||||||||| || ||||| || |||||||||||||  |||||||| ||||| || ||||
gtaatgggaggtgtgataagattcctcctcatctggtgtattaaatataattgtatgatgttgaattctgtaattagatctattgactgg--tcaaaataaaaaatgtggtttgaattagtttcattctaagtgtagtgtgcttattgtgcggttttgcttttccatttagGTGATTGATTACAAAACACAGCAGGCTAGGCTCTTCCCTTTGCTGGCTTCTGCTTATGCTTTCAGATTTGTGGGTGGGTGGCTGAAATGGCTTTATATGG

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA01G41600.1 (Glycine max), 3'ss of exon 7

----------------------------------------------------------gaatcaactgcccgcccagtgttaccacctgtgcttaacatggaaaatgcatctg-tcggttaccaacaaaaggtgtctaacatatt-caagctggttaca----gGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCAGCATATGCATTTAGATTTGTGGGTGACTGGCTGAAGTGGCTATACATGG
                                                             | || | |      ||   ||    |||  |  || |   ||| ||  | |  |  ||| |   | ||  ||  |   | ||||    | |  || ||    |||  |||||||||| || || ||    || ||||| || ||||||||||| || ||||| || ||||||||||| || |||||||| ||||| || ||||
gtaatgggaggtgtgataagatccctcctcatctggtttattaaatataattgtatgatgttgaattccgtatttagatctattgactggtcaaaataaaaaaattggttttaattagtttcattctaagtgtagcgtgcttattgtgcggtttttccatttagGTGATTGATTACAAAACACAGCAGGCTAGGCTCTTCCCATTGCTGGCTTCTGCTTATGCTTTCAGATTTGTGGGCGAGTGGCTGAAATGGCTTTATATGG

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 6

------------------------------------gaatcaactgcccg---cccagt---gttaccacctgtgcttaacatggaaaatg--catctgtc--ggttaccaacaaaaggt---gtctaacatattcaagctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCAGCATATGCATTTAGATTTGTGGGTGACTGGCTGAAGTGGCTATACATGG
                                     ||     |  | |   |  |||   || |  | |    ||  | || ||| |||  |||| |||  |   |  |||| |  |    ||     || ||        |  |||||  || |||| || ||||| || | |||  | |||||  ||||||| || |||||||||||| | ||||| || || |||||||||||||| ||||  |
gtattcaacaaatctcactattcataactatggggcaaaaatgttttctgtaacttagttaagtaagaatccaatctctagatagaatatggtcatcagtcatgaccataaacatagagaccagttattgatgttgttataattggcagGTGATTAATTATAAAACTCAGCAGAACAGGTTGTTTCCTCTGCTGGCATCTGCATATGCATTTCGGTTTGTAGGGGAATGGCTGAAGTGGCTCTACACTG

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 5

gaatcaactgcccgcccagtgttaccacctgtgc-ttaacatggaaaatgcatctgtcggttaccaacaaaaggtgtctaacatattca------agctggt-tacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCAGCATATGCATTTAGATTTGTGGGTGACTGGCTGAAGTGGCTATACATGG
               | || |||  |  | |||  ||  ||     ||  ||  | |  | |   || || | ||   |||   |||        |  |||| |  ||||  |||||||||| ||||| ||||| || |||||||| ||||||||||| || ||||| || |||||||| ||| | ||| |||| |||||||| ||||
--------gagatatctagggttttctgcagtggattttcaaaattaaatcacttcttagctctaaagaagatgtaattaatggattttctgtttacttggtctttagGTGATTGATTACAAAACTCAGCAAAGTAGGCTCTTTCCTTTGCTGGCTTCTGCCTATGCTTTCAGATTTGTTGGTCAGTGGTTGAAATGGCTATATATGG

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|211453990|gb|FL038183.1|FL038183

EST:     GTTTGGCTCTCAAGATGGTGGACCTGAGACTAAG                         GTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA
genomic: GTTTGGCTCTCAAGATGGTGGCCCTGAGACTAAGgtattctata ... ctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA

EST: gi|211453988|gb|FL038181.1|FL038181

EST:     GCGCCATCCGAAAGCAGTTTGGCTCTCAAGATGGTGGACCTGAGACTAAG                         GTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA
genomic: GCGCCATCCGAAAGCAGTTTGGCTCTCAAGATGGTGGCCCTGAGACTAAGgtattctata ... ctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA

EST: gi|211453987|gb|FL038180.1|FL038180

EST:     GCGCCATCCGAAAGCAGTTTGGCTCTCAAGATGGTGGACCTGAGACTAAG                         GTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA
genomic: GCGCCATCCGAAAGCAGTTTGGCTCTCAAGATGGTGGCCCTGAGACTAAGgtattctata ... ctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA

EST: gi|78089952|gb|DV518326.1|DV518326

EST:     GCGCCATCCGAAAGCAGTTTGGCTCTCAAGATGGTGGCCCTGAGACTAAG                         GTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA
genomic: GCGCCATCCGAAAGCAGTTTGGCTCTCAAGATGGTGGCCCTGAGACTAAGgtattctata ... ctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA

EST: gi|211132734|gb|FL016682.1|FL016682

EST:     GCGCCATCCGAAAGCAGTTTGGCTCTCAAGATGGTGGACCTGAGACTAAG                         GTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA
genomic: GCGCCATCCGAAAGCAGTTTGGCTCTCAAGATGGTGGCCCTGAGACTAAGgtattctata ... ctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA

EST: gi|211453989|gb|FL038182.1|FL038182

EST:     GTTTGGCTCTCAAGATGGTGGACCTGAGACTAAG                         GTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA
genomic: GTTTGGCTCTCAAGATGGTGGCCCTGAGACTAAGgtattctata ... ctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA

EST: gi|211132737|gb|FL016685.1|FL016685

EST:     GCGCCATCCGAAAGCAGTTTGGCTCTCAAGATGGTGGACCTGAGACTAAG                         GTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA
genomic: GCGCCATCCGAAAGCAGTTTGGCTCTCAAGATGGTGGCCCTGAGACTAAGgtattctata ... ctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCA

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: 385

AGATGCTTCTAAGGCTTTGTCCCGTGCTGTTTGCATTGCTGTACGATACAGCGCCATCCGAAAGCAGTTTGGCTCTCAAGATGGTGGCCCTGAGACTAAGgtattctata ... ctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCAGCATATGCATTTAGATTTGTGGGTGACTGGCTGAAGTGGCTATACATGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1058

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 785

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1707

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aatgcatctgtcggttaccaacaaaaggtgtctaacatattcaagctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCAGCATATGCATTTAGATTTGTGGGTGACTGGCTGAAGTGGCTATACATGG

                             gtctaac  putative branch site (score: 1707)
                                taacatatt  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatcaactgcccgcccagtgttaccacctgtgcttaacatggaaaatgcatctgtcggttaccaacaaaaggtgtctaacatattcaagctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCAGCATATGCATTTAGATTTGTGGGTGACTGGCTGAAGTGGCTATACATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
-aatcaac
- - - - tgcccgc
- - - - - - - - - - - taccacc
- - - - - - - - - - - - - - -tgtgctt
- - - - - - - - - - - - - - - - - - - catggaa
- - - - - - - - - - - - - - - - - - - - - - - - gcatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa