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

gtaagttttggatattcatttttttcatgttggtagttgtgtgtgcctttgttctaagtcttgaaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGAGTACTACAGCAAGTGGCCTAGGAGGGTTGGGTTCAGCAGATTTGGGAAG

Basic information

species	Zea mays
transcript	GRMZM2G127101_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G127101_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g03920.4 (Oryza sativa), 3'ss of exon 2

---------------------------------gtaagttttggatattcatttt----tttcatgttggtagttgtgtgtgcctttgttctaagtcttgaaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGAGTACTACAGCAAGTGGCCTAGGAGGGTTGGGTTCAGCAGATTTGGGAAG
                                 ||| |||||         ||||    |   |  || | || || |  |  || ||  ||||  | | ||||||||||||||  |||| || |||||| ||||| ||||||| | || |||||  |||||| | |||||  ||||||||||||||||  ||||  ||||||||||| |
gtaagttttgtgtactttgttttttattttggtgtatgttttcttgtcctgttttggtatcctagattcgcagatgggattctctctga-ctaatacgt-aaatcaacagCTGGAGCTGCACAGGGAGCAACAAGGCCCTCTCCAGTTACCAATGCAAGGAGTGCCACAGCTGGTGGCCTAGGAGGGTTAAGTTCTACAGATTTGGGAGG

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|211419237|gb|FK977453.1|FK977453

EST:     GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATG                         CTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA
genomic: GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATGgtaagttttg ... aaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA

EST: gi|32929284|gb|CF034096.1|CF034096

EST:     GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATG                         CTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA
genomic: GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATGgtaagttttg ... aaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA

EST: gi|211419235|gb|FK977451.1|FK977451

EST:     GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATG                         CTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA
genomic: GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATGgtaagttttg ... aaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA

EST: gi|78107355|gb|DV525773.1|DV525773

EST:     GGGGCTCAAATG                         CTGGCTCTGCCCAAGGAGCAGCAA-GTCCCTCTCTTGCTAGCAATGTTAGG
genomic: GGGGCTCAAATGgtaagttttg ... aaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGT-CCTCTCCTGCTAGCAATGTTAGG

EST: gi|32928529|gb|CF033341.1|CF033341

EST:     GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATG                         CTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA
genomic: GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATGgtaagttttg ... aaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA

EST: gi|211419234|gb|FK977450.1|FK977450

EST:     GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATG                         CTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA
genomic: GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATGgtaagttttg ... aaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA

EST: gi|194717035|gb|FK934188.1|FK934188

EST:     GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATG                         CTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA
genomic: GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATGgtaagttttg ... aaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA

EST: gi|211419238|gb|FK977454.1|FK977454

EST:     GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATG                         CTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA
genomic: GTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATGgtaagttttg ... aaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGA

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: 230

AGAGACTCAGCTGCAAATGGAACAACTAGAGCTTCAGACCCCACATCAGGGTCTCCAGCTCCAAATACTAATCCACTTCCGAATCCTTGGGGCTCAAATGgtaagttttg ... aaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGAGTACTACAGCAAGTGGCCTAGGAGGGTTGGGTTCAGCAGATTTGGGAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 362

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 337

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttttttcatgttggtagttgtgtgtgcctttgttctaagtcttgaaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGAGTACTACAGCAAGTGGCCTAGGAGGGTTGGGTTCAGCAGATTTGGGAAG

                                          ttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttggatattcatttttttcatgttggtagttgtgtgtgcctttgttctaagtcttgaaatcaacagCTGGCTCTGCCCAAGGAGCAGCAAGGTCCTCTCCTGCTAGCAATGTTAGGAGTACTACAGCAAGTGGCCTAGGAGGGTTGGGTTCAGCAGATTTGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT