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

gtaaaatctgtgcactttatgtcttttacaattcttcttgtaacctaatagcagtgcatgactgatgctttgttgttttgtgttcataattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGACTGTGATCACTACATCAACAATAGCAAGGCCATAAAAGAGGCTATGTGTT

Basic information

species	Zea mays
transcript	GRMZM2G177631_T01
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G177631_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 8

gtaaaatctg-tgcactttatgtcttttacaattcttcttgtaacctaatagcagt-gcat-gactgatgctttgttgttttgtgttcataattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGACTGTGATCACTACATCAACAATAGCAAGGCCATAAAAGAGGCTATGTGTT
||||||  |  | ||| | ||||||  ||  | | | | ||||   | | |||  | |||  |  |||     | || | |    ||  |  |||| ||||||| |||||||||||  | || |||||| ||||||||||||||||||| ||||||||||||||||||||||||||||||||||  || || |||||||
gtaaaagatccttcacataatgtctcgtatcaatttccatgtagatttacagccttagcaccgtttgacatggttttctctctctttgttgtttgacagGTCCGCGTCTCTGCTGTTCTTTCGAATGCTCCATACCTATTGAACTTGGATTGTGATCACTACATCAACAATAGCAAGGCCATAAGGGAAGCGATGTGTT

upper sequence: GRMZM2G177631_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA06G47420.1 (Glycine max), 3'ss of exon 11

----------------------gtaaaatctgtgcactttatgtcttttacaattcttcttgtaac---ctaatagcagtgcatgactgatgctttgttgttttgt----gttcataattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGACTGTGATCACTACATCAACAATAGCAAGGCCATAAAAGAGGCTATGTGTT
                      | |        | |  ||  |     | ||||  ||  || ||    |||||   ||||||    |  |  | | ||  |||||    | |   |  | | ||||  | || ||||||||  | ||||||||  | |   | ||||||||||||| | |||| | |||||||||||||||||   ||| |||||| |||||||
gtaagcaacacattaaaataatgaaggtgacaagaagcttgagaaagctccaatatttaatgcaatgatctaatt-tagtgcaaactttctaatctatttctttgttgatgattccatctaacagGTGAGAGTGTCTGCTGTGCTTTCAAATGCGCCTTTTGTGTTGAACTTGGACTATAATCATTGCATCAACAATAGCAAGGTTGTAAGAGAGGCAATGTGTT

upper sequence: GRMZM2G177631_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv18s0122g00120.t01 (Vitis vinifera), 3'ss of exon 9

gtaaa-atctgt---gcactttatgtcttttacaattcttcttgtaacctaatagcagtgcatgactgatgctttgttgttttgtg---ttcataattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGACTGTGATCACTACATCAACAATAGCAAGGCCATAAAAGAGGCTATGTGTT
||||| ||  ||   ||      ||  ||    |  |  |  || |  |||  |  |    || | |  | | ||  | ||   ||   | |  |    ||||||||| |||||||||||  |  |||||||  |||| || ||||||||||| ||||||||||||||||| || || |||||  | |  ||| |||||||||
gtaaatattagtaaagcgacaactgaattccgtatgttcttatgcagtctacaaaaatcttataatttttacctttatcttcattggcttgcccatcaaatagGTCCGAGTCTCTGCTGTGCTCACAAATGCACCATATCTGTTGAACTTGGATTGTGATCACTACATCAATAACAGTAAGGCTCTTAGGGAGTCTATGTGTT

upper sequence: GRMZM2G177631_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 9

gtaaaatctgtgcactttatgtcttttacaattcttcttg-taacctaatagcagtgcatgactgatgctttgttgttttgtgttcataattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGACTGTGATCACTACATCAACAATAGCAAGGCCATAAAAGAGGCTATGTGTT
        | || |  ||       | |||  | |||| | |  ||| |||    ||  ||| |  |  ||  | ||    |  |  |     | ||||||| |||||||||||  |  | |||||  | || |||||||| ||||| |||||||||||| ||||||| ||||||||  | || ||||| |||||||
-------gtatgtagcttggtaaaatcacatctattctaggtgtcctgataaagatgtctgaattttatttcctggtgggcttattctttaaaacagGTCCGAGTCTCTGCTGTTCTTACGAATGCACCTTATCTATTGAATTTGGATTGTGATCACTACTTCAACAACAGCAAGGCTCTCAAGGAGGCAATGTGTT

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|32846630|gb|CD986311.1|CD986311

EST:     AGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTG                         GTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGAC
genomic: AGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTGgtaaaatctg ... taattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGAC

EST: gi|91873599|gb|EB403556.1|EB403556

EST:     AGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTG                         GTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGAC
genomic: AGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTGgtaaaatctg ... taattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGAC

EST: gi|211336415|gb|FL383134.1|FL383134

EST:     AGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTG                         GTCCGTGTCTCTGCTGTCTTATCAAATGCTGCGTACCTACTGAACTTGGAC
genomic: AGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTGgtaaaatctg ... taattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGAC

EST: gi|211101700|gb|FL470685.1|FL470685

EST:     AGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTG                         GTCCGTGTCTCTGCTGTCTTATCAAATCCTGCATACCTATTGAACTTGGAC
genomic: AGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTGgtaaaatctg ... taattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGAC

EST: gi|32849039|gb|CD988720.1|CD988720

EST:     AGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTG                         GTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGAC
genomic: AGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTGgtaaaatctg ... taattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGAC

EST: gi|32929817|gb|CF034629.1|CF034629

EST:     AGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTG                         GTCCGTGTCTCTGCTGTCTTATCAAATGCTCCATACCTATTGAACTTGGAC
genomic: AGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTGgtaaaatctg ... taattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGAC

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: 280

TGATGTGGAAGGAAATGAGTTGCCTCGCCTGGTTTATGTCTCGAGAGAAAAGAGGCCAGGTTATAACCATCACAAGAAGGCTGGTGCCATGAATGCACTGgtaaaatctg ... taattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGACTGTGATCACTACATCAACAATAGCAAGGCCATAAAAGAGGCTATGTGTT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 517

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 454

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 613

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aacctaatagcagtgcatgactgatgctttgttgttttgtgttcataattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGACTGTGATCACTACATCAACAATAGCAAGGCCATAAAAGAGGCTATGTGTT

                                            ataattgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatctgtgcactttatgtcttttacaattcttcttgtaacctaatagcagtgcatgactgatgctttgttgttttgtgttcataattgatagGTCCGTGTCTCTGCTGTCTTATCAAATGCTGCATACCTATTGAACTTGGACTGTGATCACTACATCAACAATAGCAAGGCCATAAAAGAGGCTATGTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG