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

...tttgtgtcactggtccagtctttgtggagttatggtttgaaaatgataccactgtcgtaagtttgctctagttcaccccatcttttttctaatgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATATACAGAAGCTTCATATCCGCACAATCCCCCTTAATGAACAAGCACGTCGC

Basic information

species	Zea mays
transcript	GRMZM2G402002_T01
intron #	16
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 16

--------tttgtgtcactggtccagtcttt-gtggagttatggtttgaaaatgataccactgtcgtaagtttgctctagttcaccccatcttttttctaatgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATATACAGAAGCTTCATATCCGCACAATCCCCCTTAATGAACAAGCACGTCGC
        | ||   |  |   |   || || || |||   |  |||  ||||||    | | |  ||  ||||    |||  |    |  ||       || |  ||| ||||||||||||||||| |||||||| ||||||||||| |||||||| || ||||||||||||||||| ||||||||| | ||||||||||||||||||
agttatgctctggaaccttctccatctcattagtagagcatttatttcgaaatgacg--attatactatttttgtagcagtaaattgaacttt-------atcttgcagCCTTGCAATTGCTAAAGAAGGTGAACTCTCAATTGGAACCATCGATGACATCCAGAAGCTTCATATCCGTACAATCCCCTTGAATGAACAAGCACGTCGC

upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 16

-------------------tttgtgtcactggtccagtctttgtggag--ttatggt----ttgaaaatgataccact-gtcgtaag----tttgctctagttcac-cccatcttttttc--taa-tgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATATACAGAAGCTTCATATCCGCACAATCCCCCTTAATGAACAAGCACGTCGC
                   ||||  | ||| |    || |   |      || || |    ||| |  |  ||| | |    ||||     ||| ||   | | || | |||||  | |   ||| ||  ||||| | |||||||| ||||| ||||| ||| | ||||| ||||| ||||||||||| || |||||||| ||| | || || ||    || || ||||| || 
gtatcttggtctttgttagtttgacttactagagttgtttacatatccccttgtgctgttcttggatcttgtacaatttaatgtaaaatcttttactggtgatgacactcatctactgttaataactgaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACTATTGATGATATACAAAAACTTCATATTCGCTCTATTCCGCTGGGGGAGCACGCACGACGT

upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA12G08330.1 (Glycine max), 3'ss of exon 3

-------------------tttgtgtcactggtccagtctttgtggag--ttatggt----ttgaaaatgataccact-gtcgtaag----tttgctctagttcac-cccatcttttttc--taa-tgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATATACAGAAGCTTCATATCCGCACAATCCCCCTTAATGAACAAGCACGTCGC
                   ||||  | ||| |    || |   |      || || |    ||| |  |  ||| | |  | ||||     ||| ||   | | || | |||||  | |   ||| ||  ||||| | |||||||| ||||| ||||| ||| | ||||| ||||| ||||||||||| || |||||||| ||| | || || ||    || || ||||| || 
gtatcttggtctttgttagtttgacttactagagttgtttacatatccccttgtgctgttcttggatcttgtacaatttattgtaaaatcttttactggtgatgacactcatctactgttaataactgaaacagTTTGGCAATTGCAAAAGAAGGTGAGCTTACTATTGGCACTATTGATGATATACAAAAACTTCATATTCGCTCTATTCCGCTGGGGGAGCACGCACGACGT

upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 16

tttgtgtcactggtccagtctttgtggagttatggtttgaaaatgatac-cactgtcgtaagtttgctctagttcaccccatcttttttctaatgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATATACAGAAGCTTCATATCCGCACAATCCCCCTTAATGAACAAGCACGTCGC
     || |    |    |   | ||   || |  ||||  |   |    || ||| || |  |         |  | | |  | | ||| | ||   |||||| |||||||| |  ||||| |||||| ||||||| || |||||||| || ||||||||||| || ||||| || ||| ||   || || || ||||| 
-----gtaaactatatttttcctctgttattttcctttgggatcaaagtacattgtggtgaaatc--------tggctctacttctcttccattg--gcagTCTAGCAATTGCAAGGGAGGGCGAACTTACAATTGGTACCATCGATGACATTCAGAAGCTTCACATACGCACCATTCCCATTGGAGAGCATGCTCGTCGG

upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 16

tttgtgtcactggtccagtct-----ttgtggagttatggtttgaaaatgataccactgtcgtaagtttgctctagttcaccccatcttttttctaatgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATATACAGAAGCTTCATATCCGCACAATCCCCCTTAATGAACAAGCACGTCGC
    ||    |||| ||          || | || |    || | ||||||||  | ||   ||||      |||  |     | | | |   |   | | |||| ||||||||||| ||||| ||||| ||| |||| || || || |||||||| ||||||||||| |||||| | ||||| |||   || || || || |||
-ccatgagcttggtacaagtaagaggctgagaagatgaaatt-gtaaatgatattattgggttaag---agactaactggtggcttttctccccctttcttacagCCTTGCAATTGCCAAAGAAGGTGATCTTACAATCGGTACCATTGATGATATCCAGAAGCTTCACATCCGCTCTATCCCACTTGGGGAGCATGCTCGCCGC

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|87152613|gb|DY397402.1|DY397402

EST:     CGCTTTTCCAGACAG                         TCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATAT
genomic: CGCTTTTCCAGACAGgtttgttccc ... aatgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATAT

EST: gi|78088360|gb|DV516753.1|DV516753

EST:     AAAGAGGTTAATCATATGTGCCCTTTCAATACAGCCGCTTTTCCAGACAG                         TCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATAT
genomic: AAAGAGGTTAATCATATGTGCCCTTTCAATACAGCCGCTTTTCCAGACAGgtttgttccc ... aatgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATAT

EST: gi|18650043|gb|BM498862.1|BM498862

EST:     CGCTTTTCCAGACAG                         TCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATAT
genomic: CGCTTTTCCAGACAGgtttgttccc ... aatgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATAT

EST: gi|19822804|gb|BQ048828.1|BQ048828

EST:     CGCTTTTCCAGACAG                         TCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATAT
genomic: CGCTTTTCCAGACAGgtttgttccc ... aatgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATAT

EST: gi|24767501|gb|CA402643.1|CA402643

EST:     AAAGAGGTTAATCATATGTGCCCTTTCAATACAGCCGCTTTTCCAGACAG                         TCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATAT
genomic: AAAGAGGTTAATCATATGTGCCCTTTCAATACAGCCGCTTTTCCAGACAGgtttgttccc ... aatgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATAT

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), 48 (downstream exon)
Score: 458

CTGTCATCTATAGCAGCAATAAGAAGCTTCTCTACAGCAATGTCAATTTGAAAGAGGTTAATCATATGTGCCCTTTCAATACAGCCGCTTTTCCAGACAGgtttgttccc ... aatgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATATACAGAAGCTTCATATCCGCACAATCCCCCTTAATGAACAAGCACGTCGC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 302

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 196

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 265

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ataccactgtcgtaagtttgctctagttcaccccatcttttttctaatgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATATACAGAAGCTTCATATCCGCACAATCCCCCTTAATGAACAAGCACGTCGC

                                         ttctaat  putative branch site (score: 265)
                              ccccatcttttttcta  CT-rich tract
                                  atcttttttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtgtcactggtccagtctttgtggagttatggtttgaaaatgataccactgtcgtaagtttgctctagttcaccccatcttttttctaatgtcacagTCTTGCAATTGCTAAAGAGGGTGAACTTTCAATTGGAACTATCGATGATATACAGAAGCTTCATATCCGCACAATCCCCCTTAATGAACAAGCACGTCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - -ctggtcc
- - - - - - - - - - - - - - - - - - - gaaaatga
- - - - - - - - - - - - - - - - - - - - - - - - ccactgt