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

...aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcattatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC

Basic information

species	Zea mays
transcript	GRMZM2G038126_T02
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 5

aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcct----caccctgaa--tgctcctcgcattatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
  | |||  ||| | || | ||| | | | |    | | |||||   |   ||  |  |||  | |        |||||  |  |  |    || ||||||| ||||||||||||||||||||||||||||| ||||||||||| |||||||| || ||||| ||||||||||||||||| |||||||| |||||||||||     
tttactctctgc-tcagcttttgctcaataa----atactgtaagcatttatattcgctttcccttgtgctgttctgaaattcattgtgatgttctgttttt-cagATTGCTGCTATCTGTCAAGAAGCTGGTATGCATGCTGTGCGCAAAAATCGGTATGTTATCCTCCCCAAGGACTTCGAGAAGGGTTACCGAACCAATGTCA

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 5

aatgctccttgcattagttattggttattgacctgac-aatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcattatgtt-tttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
|  | |   ||   ||  ||      |       | | ||||| ||  ||  |    | | | |   ||   | | |  |    | ||  || |   | |||||  | ||||| |||||||||||||| ||||||||||| ||||| ||  |||||||||| || ||||||||||| |||||||| ||| | || |||    
agaggtagctgtgataaataagaaagacgattaagtctaatgtcaa--taaatgtgatatatataaacagttttattatttgatgaatgttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCCAAGGACTTCGAGAAGGGTTACAGGACAAACGTGA

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 5

aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcattat-----gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
  || |   |  ||   | || |   ||||  |   |  |  |    |  ||||  | | | |    |  | |  |  || |   || ||     ||   | |||||  | ||||| |||||||||||||| ||||||||||| ||||| ||  |||||||||| || || |||||||| |||||||| ||  | || |||    
--tg-tgaatatatgcctgatagaagattg--ccatctctacaggtctttgtaatatatatatatataaacagttttatcatttgatgattgttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCAAAGGACTTCGAGAAGGGTTATAGGACAAACGTGA

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 5

aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctt--tttttcctcaccctgaatgctcctcgcattat--gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
|||          | | | | || | ||  |  |    || |||||  ||||     |  | | |   ||   | | |  |    | ||| |  ||   | ||||| || || || |||||||||||||| ||||||||||| ||||| ||  |||||||||| || || |||||||| |||||||| ||| | || |||    
aataagttaaatgtcaataaatg-tgatatatatat--atataaaaacaggtctttgtaatatataaacagttttattatttggtg-attgttggtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCGAAGGACTTCGAGAAGGGTTACAGGACAAACGTGA

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 5

aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcat----tatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
||    |   | |    | || ||||    |  |       | |  | |  ||| |   |||  |      ||| || |  |  ||     | |   | | |||||||||||||| |||||||||||||| ||||||||||| ||||| ||||||||||| || ||||||||||||||||||||||| || ||||||||     
aaccagcggagaaactctgataggttcccaaggtt-tttcattatttcaaataaacgaatttctcatg---tgagtgtttttaacacaatctgtacgtatgcagATTGCTGCTATTTGTCAAGAAGCTGGGATGCATGCTGTTCGCAAGAACCGATATGTAATTCTCCCCAAGGACTTTGAGAAGGGTTATCGAACCAATGTGA

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 5

aatgctccttgcattagttattggt--tattgacctgacaatgtaa-aattaggtaacctttttttcctcaccctgaatgctcctcgcattatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
 ||| |   | ||   || | |  |  ||||          ||||  |  | | |     | |  | |  | |    ||| |       | |||      |||||| |||| |||||||| || ||||| |||||||| ||| | || || || ||||| ||  | |||||||| ||||||||||||||| || |||||    
tatgttgagttcagctgtaaattatagtattaggtcaggtctgtattagctggatttgtatgtgctgcatatctgatatgattgatttgtcatg---acgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGTTATGTGATTTTGCCCAAGGATTTTGAGAAGGGCTACAGATCCAACGTCA

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 5

aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcattatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
                                               |||  | || ||| |      |  |          ||||||   ||| | ||||||||||| || |||||||| || ||||||||||| ||  | || || || || || || || |||||||||||||||||||||||| | ||||||    
----------------------------------------------gtagagagccgtttgtcttgggcttta---ctctgacgcatttcctttatccagATTGCTGCGATATGTCAAGAGGCAGGCATGCATGCGGTGAGGAAGAATCGCTACGTTATTCTTCCCAAGGACTTTGAGAAGGGCTACAGGACCAACGTGA

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|67017682|gb|CO446431.1|CO446431

EST:     TTGATTTGGAAGACTATGTTTNCAGACCGGATAAGATCAGTGCTGCTGAT                         ATTGCTGCTATCTGTCAAGAAACTGGCATGCATGCTGTNNCGCAAAA
genomic: TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTC-CGCAAAA

EST: gi|32835304|gb|CD974982.1|CD974982

EST:     TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGAT                         ATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGA
genomic: TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGA

EST: gi|6194636|gb|AW146740.1|AW146740

EST:     TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGAT                         ATTGCTGCTATCTGTCAAGAANCTGGCATGCATGCTGGCCGCAAAAACCGA
genomic: TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGA

EST: gi|32846623|gb|CD986304.1|CD986304

EST:     TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGAT                         ATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGA
genomic: TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGA

EST: gi|18964972|gb|BM661316.1|BM661316

EST:     TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGAT                         ATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCT
genomic: TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCT

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), 48 (downstream exon)
Score: 130

GTCTGCACTGCCAAAATGAACCTGAGTGACGAGGTTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 165

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 167

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 217

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attaggtaacctttttttcctcaccctgaatgctcctcgcattatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC

                 tcctcac  putative branch site (score: 217)
                                            tgttttt  putative PPT
                                        attatgtttttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcattatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC

- tgctcct
- - -tccttgc
- - - - - - - - - - - - - - tgacctg