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

gtttgtgaaagtctatcttctatcctgttttatcagttatttttggttctctgatctttacctgacaatgctggcacgcttcatgaatgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTATTGTGGAGAGTTTGATAATGTTGGCGCTCTTT

Basic information

species	Zea mays
transcript	GRMZM5G899390_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G899390_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G42050.1 (Glycine max), 3'ss of exon 2

------gtttgtgaaagtctatcttctatcctgttt-tatcagttatttttggttc-tctgatctttacctgacaatgctggcacgcttcatgaatgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTATTGTGGAGAGTTTGATAATGTTGGCGCTCTTT
      | || |   | | || | | | || | | | | | | || ||     ||| |||||||    ||| |   | ||  |    ||  |   | |   ||||| || || ||||| |||||||| |||||  || |||||||||| || || ||||| |||||||||||| |||| || ||||| |||| ||| ||  | |
ttccttgctt-tcttactttaacctttgtcttttatgtgttacttcttccaacttcctctgatcaaggcctcattttactttcctatttttt---ttttaatagGTTGTGGAGGATGGATATGAGTTTTTTGCTAAAAGAAGATTAGTCACGATATTTTCTGCTCCAAATTATGGTGGGGAATTTGACAATGCTGGTGCGTTGT

upper sequence: GRMZM5G899390_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G05580.1 (Arabidopsis thaliana), 3'ss of exon 2

----------------------------------------------gtttgtgaaa--gtctatcttctatcctgttttatcagt-tatttttggtt-------ctctgatctttacctgacaa--tgctggcacgcttcatgaatgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTATTGTGGAGAGTTTGATAATGTTGGCGCTCTTT
                                               | |||  ||  || |  | | | |  | | || | | | |     |           || | ||    ||||  |||  |  || |  |         |||    |||| || |||||||| |||||||| || ||| |||| || ||||| ||||| || ||||||||||| ||| | ||||||||||| ||||  || ||  | |
gtaaatagacttccatagtgatcaaaactagaaccaaatggtccaactctgtagaaatgtttgacatttgttgtatcttgtgaatatgggcataaaggaaaagacttttatgagaaccttccaagatattgacttgtgagggacgtgtttgcagGTAGTGGAAGATGGGTATGAGTTTTTCGCAAAACGGAGGTTAGTCACAATATTCTCAGCTCCAAACTATGGAGGAGAGTTTGACAATGCCGGTGCATTAT

upper sequence: GRMZM5G899390_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G27840.2 (Arabidopsis thaliana), 3'ss of exon 2

-------------------------gtttgtgaaagtctatcttctatcctgttttatcagttatttttggttctctgatctttac-----ctgacaatgctgg-cacgcttcatgaatgtccc---tagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTATTGTGGAGAGTTTGATAATGTTGGCGCTCTTT
                            ||||||| | |   |  |    || || | |  || |   |    ||     ||||       || || ||   || || |  | |||  | |       |||| || ||||| || |||||||| || ||| |||| |||||||| || || || ||||||||||| ||| |||| |||||||| || | ||| ||  | |
gtaaaacaaacaagacctcctcgaaacctgtgaaattgttcttgatggtttgatt-agcgtttgtccataaagctagagactttttgaattcttaccatatcggacatgtgtaatggttttgtgatgcagGTAGTAGAAGACGGGTATGAGTTTTTCGCAAAACGGAGATTAGTCACGATATTCTCAGCTCCAAACTATGGTGGGGAGTTTGACAACGCTGGTGCGTTAT

upper sequence: GRMZM5G899390_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0060g01750.t01 (Vitis vinifera), 3'ss of exon 2

gtttgtgaaagtctatcttctatcctgttttatcagttatttttggttctctgatctttac--ctgacaatgctggca-----cgcttcatgaatgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTATTGTGGAGAGTTTGATAATGTTGGCGCTCTTT
  |  |   || | | |||   || | | |    | |  | | || |    | ||  | |   |      | | | |      || |  | |         ||||||| || ||||| ||||| ||||||||  ||||| ||||||| ||||| |||||||| ||||| ||| ||||||||||||||||||  || |||||||
--tcataccag-ccagcttgagtcatatctagggactggtgtctgataacatcatactaaaaacaagtggtccagactaaaatcgttctaagctgaattgcagGTGGTGGAGGATGGATATGAATTCTTTGCTAAACGACGATTAGTCACAATTTTTTCAGCACCAAACTATGGTGGAGAGTTTGATAATGCCGGTGCTCTTT

upper sequence: GRMZM5G899390_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S97_286V6.1 (Physcomitrella patens), 3'ss of exon 3

---gtttgtgaaagtctatctt--ctatcctgttttatcagttatttttggttctctgatctttacctgacaatgctggcacgcttcatgaatgtccc---tagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTATTGTGGAGAGTTTGATAATGTTGGCGCTCTTT
   |  | ||||  ||         |  | ||| |  ||    |   |   || | |  |||||   | || ||||||    |  |   | ||||  |    |||| || || ||||| ||||| || || ||  | ||   | | || || || ||||| ||||||||||||||||| || ||||||||||  || ||  |  
gacgaatttgaacctccgatgcgattgacatgtctcttccaccaccat-acttttatattctttgtat-actatgctgatctgtgtg--ggatgttacatacagGTAGTAGAGGATGGTTATGAATTTTTCGCTAAGCGCCAACTGGTTACCATTTTTTCTGCTCCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA

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|67014742|gb|CO443491.1|CO443491

EST:     TAGAGTTTTTGGAGAAGAATGATCTCGATCTTATATGCCGAGCTCATCAG                         GTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC
genomic: TAGAGTTTTTGGAGAAGAATGATCTCGATCTTATATGCCGAGCTCATCAGgtttgtgaaa ... atgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC

EST: gi|9794844|gb|BE553152.1|BE553152

EST:     TAGAGTTTTTGGAGAAGAATGATCTCGATCTTATATGCCGAGCTCATCAG                         GTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC
genomic: TAGAGTTTTTGGAGAAGAATGATCTCGATCTTATATGCCGAGCTCATCAGgtttgtgaaa ... atgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC

EST: gi|71315601|gb|DR794411.1|DR794411

EST:     TAGAGTTTTTGGAGAAGAATGATCTCGATCTTATATGCCGAGCTCATCAG                         GTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC
genomic: TAGAGTTTTTGGAGAAGAATGATCTCGATCTTATATGCCGAGCTCATCAGgtttgtgaaa ... atgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC

EST: gi|78074892|gb|DV503326.1|DV503326

EST:     TAGAGTTTTTGGAGAAGAATGATCTCGATCTTATATGCCGAGCTCATCAG                         GTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC
genomic: TAGAGTTTTTGGAGAAGAATGATCTCGATCTTATATGCCGAGCTCATCAGgtttgtgaaa ... atgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC

EST: gi|32847130|gb|CD986811.1|CD986811

EST:     TAGAGTTTTTGGAGAAGAATGATCTCGATCTTATATGCCGAGCTCATCAG                         GTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC
genomic: TAGAGTTTTTGGAGAAGAATGATCTCGATCTTATATGCCGAGCTCATCAGgtttgtgaaa ... atgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC

EST: gi|78106362|gb|DV524780.1|DV524780

EST:     TAGAGTTTTTGGAGAAGAATGATCTCGATTTTATATGCCGAGCTCATCAG                         GTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC
genomic: TAGAGTTTTTGGAGAAGAATGATCTCGATCTTATATGCCGAGCTCATCAGgtttgtgaaa ... atgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC

EST: gi|9824892|gb|BE574989.1|BE574989

EST:     CTTATATGCCGAGCTCATCAG                         GTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC
genomic: CTTATATGCCGAGCTCATCAGgtttgtgaaa ... atgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATC

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: 95

GGGGGAGAGTGACAGGGGTGTCTCGTGTACGTTTGGTGCAGATAAACTTGTAGAGTTTTTGGAGAAGAATGATCTCGATCTTATATGCCGAGCTCATCAGgtttgtgaaa ... atgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTATTGTGGAGAGTTTGATAATGTTGGCGCTCTTT

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 121

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 150

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttggttctctgatctttacctgacaatgctggcacgcttcatgaatgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTATTGTGGAGAGTTTGATAATGTTGGCGCTCTTT

                  acctgac  putative branch site (score: 150)
                                              tgtccct  putative PPT
            atcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgaaagtctatcttctatcctgttttatcagttatttttggttctctgatctttacctgacaatgctggcacgcttcatgaatgtccctagGTGGTTGAAGATGGCTATGAGTTCTTTGCACAACGAAGATTAGTGACAATCTTTTCAGCTCCAAATTATTGTGGAGAGTTTGATAATGTTGGCGCTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA