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

gcaagtatctcctcacaatgtttcatcccctctccacattctcaacactcatgcggacatcatcaaattctggtaactgcatatgaaaaaaaaaccaaaatcctgacataccggggacttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC

Basic information

species	Zea mays
transcript	GRMZM2G141535_T01
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g57690.1 (Oryza sativa), 3'ss of exon 9

gcaagtatctcctcacaatgtttcatcccctctccacattctcaacactcatgcggacatcatcaaattctggtaactgcatatgaaaaaaaaaccaaaatcctgacat-accggggactt-----gtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC
                                                   ||   |  || ||    | || |   |   | |     |||   |  ||| |||| ||    |  | | |     |  ||||||||| || |||||||||||| | || ||  | |||||||||||||||||||||||||| ||||||||||| |||||||||||| | | |  |    || |
--------------------------------------------------gtgaaaatctcttcttcgtttgctccttttttttttctcaaa--tctgaattctgatattgttgctgtccttcatggcatgcagCGTCCGGTGAGCCGCCGCTGCTGCTGGCGTCGTCGGTGCACTGCGCGATGAGGGAGGCGATCAGGGCGGCCAGGAAGGAGTTCGCCGGCGCCGGAGGCTC

upper sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g57680.1 (Oryza sativa), 3'ss of exon 9

gcaagtatctcctcacaatgtttcatcccctctccacattctcaacactcatgcggacatcatcaaattctggtaactgcatatgaaaaaaaaaccaaaatcctgacataccg-gggacttgt--ttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC
                                                | |      | || ||    | ||   |||| |   |  ||  ||| | |||||   |  |     | ||    |  | |||||||| || |||||||||||| | || ||  | |||||||||||||||||||||||||| ||||||||||| |||||||||||| | | |  |  | || |
-----------------------------------------------gtgaaatcatcgtcttcttcctttgagcactgaaatcgtgaaggaaatcgaaatctgaaactgttttgtgatccatcgtggcagCGTCCGGTGAGCCGCCGCTGCTGCTGGCGTCGTCGGTGCACTGCGCGATGAGGGAGGCGATCAGGGCGGCCAGGAAGGAGTTCGCCGGCGCCGGCGGCTC

upper sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 9

gcaagtatctcctcacaatgtttcatcccctctccacattctcaacactcatgcggacatcatcaaattctggtaactgcatatgaaaaaaaaaccaaaatcctgacataccggggacttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC
               | |  || | |  ||| |  |||    |||  |  || |   |      | |   |   ||||  | |     ||||| |  ||    |    |   | | |  |  | |||||||| || |||||||||||| | || ||  | || ||||||||||||||||||||||| |||||||||||| |||  |||||| | |    |  | ||  
--------------tcgagattgc-taacctgtgaacaa---caaaccctatacaagc-----tatacattcacaacttta-acactgaaaaatctgaagctgt----tttggcgtatgtcatggcagCGTCCGGTGAGCCGCCGCTGCTGCTGGCGTCGTCCGTGCACTGCGCGATGAGGGAGGCGATCAGGGCGGCGCGGAGAGAGTTCGCCGCTGTCGGCGGCGG

upper sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g57720.1 (Oryza sativa), 3'ss of exon 2

gcaagtatctcctcacaatgtt-tcatcccctctccacattctcaacactcatgcggacatcatcaaattctggtaactgcatatgaaaaaaaaaccaaaatcctgacataccggggacttgtttgcagCGTCGGGCGA-GCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCA----GGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC------------------------------------------------
                 |  |  || ||  ||  |     ||      ||||  ||  ||| | |||      | ||  | | | |||    ||| |  || | ||   | |  |   | | || |||||||| || || |||||||| | | || ||  | |||||||||||||||||||||||||| ||||    ||||||| |||||||||||| | | |  |  | || |                                                
--------------gtgaaatcatcgtcttcttcctttgatcctttttctcaaacg--catgagcaat-----gaaatcgtaaaggaactcgaaatctgaaac-tgttttgc--gatccatcttggcagcgtccggtgaagccgccgccgctgctggcgtcgtcggtgcactgcgcgatgagGGAGGCGATCAATCAGGGCGGCCAGGAAGGAGTTCGCCGGCGCCGGCGGCTCGGCGATGACTTTCCAGATGGACGTGCCGGCGACGATGCCGGCCGTCAA

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|47962029|gb|CN844738.1|CN844738

EST:     TGAGATGTTTAACAGCGCCCCTGACAAGAAGCGTGTCCTATCTTCCAAAG                         CGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGA
genomic: TGAGATGTTTAACAGCGCCCCTGACAAGAAGCGTGTCCTATCTTCCAAAGgcaagtatct ... ttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGA

EST: gi|44900915|gb|CK827460.1|CK827460

EST:     TGAGATGTTTAACAGCGCCCCTGACAAGAAGCGTGTCCTATCTTCCAAAG                         CGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGA
genomic: TGAGATGTTTAACAGCGCCCCTGACAAGAAGCGTGTCCTATCTTCCAAAGgcaagtatct ... ttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGA

EST: gi|62525891|gb|DN828539.1|DN828539

EST:     TGAGATGTTTAACAGCGCCCCTGACAAGAAGCGTGTCCTATCTTCCAAAG                         CGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGA
genomic: TGAGATGTTTAACAGCGCCCCTGACAAGAAGCGTGTCCTATCTTCCAAAGgcaagtatct ... ttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGA

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: 27 (upstream exon), 24 (downstream exon)
Score: 4

TGGACGTACAAGATCCCCACGGTGGATAATATCCCGAAGGAGTTCAATGTTGAGATGTTTAACAGCGCCCCTGACAAGAAGCGTGTCCTATCTTCCAAAGgcaagtatct ... ttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 241

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 94

Block sizes: 46 (upstream exon), 40 (downstream exon)
Score: 51

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taactgcatatgaaaaaaaaaccaaaatcctgacataccggggacttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC

                           tcctgac  putative branch site (score: 51)
                                            cttgttt  putative PPT
       atatgaaaaaaaaacc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtatctcctcacaatgtttcatcccctctccacattctcaacactcatgcggacatcatcaaattctggtaactgcatatgaaaaaaaaaccaaaatcctgacataccggggacttgtttgcagCGTCGGGCGAGCCGCCGCTGGTTCTCGCAGCCTCGGTGCACTGCGCGATGAGGGAGGCCATCAGGGCGGCGAGGAAGGAGTTCTCGGTCAGCACCAGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG