ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtatttattcagtcttttggctttcttgctttttatttgctatttaggagtgtgtgatgtgacagtaatgcattttctctgttttaaaacaattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG

Basic information

species	Zea mays
transcript	GRMZM2G088231_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 4

-----------gtatttattcagtcttttggctttct-tgctttttatttgctatttagga-gtgtgtgatgtgacagtaat--gcattttctctgttttaaaacaattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG
                |     ||||||  ||||||| | |||  |   |  ||||| |   | |||   |||   ||| ||     ||||  |   || |||| || |  |||||||| ||||| ||||| ||||||||||| ||||| || |||||||| ||||||||||| ||||||||||| ||| ||||||||||||| ||||||||||
gtatccgatcatctcctgacttgtctttgtgctttctgtacttccttgatattattttgattgagtgcattgttggagttattaatgtttttacctcttgaaaaaaaattgaagGCTGTATGGGCATTGGGCAATGTTGCTGGTGATTCCCCTAAGTGCCGTGACCTTGTTCTTGCCAATGGTGCATTGCTGCCTCTGCTAGCACAGTTGAATG

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G04430.1 (Glycine max), 3'ss of exon 4

--gtatttattcagtcttttggctttcttgctttttatttgctatttaggagtgtgtgatgtgacagtaatgcattttctctgttttaaaacaattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG
   | || || ||    | |||   |  ||   || | ||| | |  |    ||   ||  | ||   ||| |     |||||         || |   |||| |||||||| ||||| ||||||||||| || ||||| ||||| || || |||||||||  | |||||||  |||| || ||| | |||||||||||||
gtatgttgatgcatgaatgtggtagtgctgacatt-acttgttttgaaattttggccgagcttaccagaatactaaaactctg---------aaattccagGCAGTGTGGGCATTGGGGAATGTTGCTGGTGACTCTCCTAAGTGTCGTGATCTTGTTCTCAGCCATGGTGCCCTGATCCCACTGTTGGCCCAGTTGAATG

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G16143.1 (Arabidopsis thaliana), 3'ss of exon 3

---------gtatttat---tcagtcttttggctttct-tgct-----ttttatttgctatttaggagtgtgtgatgtgacagtaatgcattttctctgttttaaaacaattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG
         || |||||   |   |||  || ||   | | ||     |||| |||| | ||  |||    |  ||||   |    |   || | |||   |     ||  |  |||||||||||||| || || ||||||||||| ||||||||   |||| | || ||||| || |   | || || ||||| ||  | ||  | ||||||||||
gtaagatatgtgtttatggttttttctcatgactcaatatactgtcaattttgtttgtt-ttcgggaacaagc-atgttctaaagcttgtttgtttcttaatcttttcatgtgtaagGCTGTGTGGGCATTAGGGAATGTTGCTGGTGATTCTCCACGGTGCAGAGATCTTGTCCTTGGTCAAGGAGCTTTGATACCATTACTCTCTCAGTTGAATG

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G06720.2 (Arabidopsis thaliana), 3'ss of exon 4

gtatttattcagtcttttggctttc---ttgctttttatttgctatttaggagtgtgtgatgtgacagtaatgcattttctctgttttaaaac--------aattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG
||||  |     |||  || ||      |  ||| | ||||  |||    || | ||  || ||| | |  ||      |    | |||| |         ||     ||||||| |||||||||||||| |||||||| ||||| ||   |||||| || |||||||| |    ||| ||  || | || |||||    ||| | ||||
gtatggaact--tctgatgactacagaatgtcttctcatttattatgagagattatgcaat-tgaaaattttgtgaaaccctgatcttaagatttcgctctaacctgcagGCTGTATGGGCTTTGGGTAACGTTGCTGGTGATTCACCACGGTGCCGTGATCTTGTTCTTGGATGTGGGGCACTGCTTCCGCTGCTCAATCAGCTTAATG

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 4

gtatt-tattcagtcttttggctttcttgctttttatttgctatttaggagtgtgtgatgtgacagtaatgc-attttctctgttttaaaacaatt--aaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG
|| |   |||  |   ||| |||   |  | |  | ||  | | |  ||| |   || ||   ||||  |||    ||  |||||   |  |  ||  || ||||||| ||||||||||| || |||||||| ||||| ||||| ||||| ||||||||| | |   |||| || |||||||||||||| || ||| | |  |
gtttcacattgtgatctttagctaggtgtcatgcttttgtcgact--ggatttcatgctg-accagttgtgccgacttgactgttaatattctctttgaacagGCTGTATGGGCTTTGGGAAACGTTGCTGGTGATTCGCCGAAATGCCGTGACCTTGTTTTAGGTCATGGGGCCTTGATGCCTCTGCTTGCGCAGCTTACGG

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ38593 (Selaginella moellendorffii), 3'ss of exon 4

gtatttattcagtcttttggctttcttgctttttatttgctatttaggagtgtgtgatgtgacagtaatgcattttctctgttttaaaacaattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG
                                      |  ||||       |||  |   | ||    | || |    | |  |   ||       |||| || |||||| | || |||||||||||||| |||||||||||||| || || ||  |    |    |||  |||||||  ||||||| ||| |||| |
--------------------------------------gtgattttttctcttgtatttccaaagcttggaatctgacatttcctggtaccgc----agGCAGTATGGGCTCTTGGCAATGTTGCTGGCGACTCTCCGAAGTGCCGAGATCTCGTCTTGAATAGCAATGCCATGATGCCGTTGCTAGCACAGCTGAACG

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|32858412|gb|CD998093.1|CD998093

EST:     ATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: ATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC

EST: gi|71440662|gb|DR821712.1|DR821712

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC

EST: gi|211385914|gb|FK983423.1|FK983423

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGA
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTT-GGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGA

EST: gi|28987202|gb|CB351514.1|CB351514

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGG
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGG

EST: gi|149111962|gb|EE191122.2|EE191122

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC

EST: gi|87151836|gb|DY396625.1|DY396625

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC

EST: gi|76021460|gb|DT948630.1|DT948630

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC

EST: gi|78179900|gb|DV550273.1|DV550273

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGA
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGA

EST: gi|211385909|gb|FK983418.1|FK983418

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGGCTTTGGGTAATGTTGCTGGCGATT
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGG-CTTTGGGTAATGTTGCTGGCGATT

EST: gi|18963328|gb|BM660373.1|BM660373

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC

EST: gi|22490161|gb|BU050084.1|BU050084

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC

EST: gi|211383281|gb|FK983411.1|FK983411

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGGCTTTGGGTAATGTTGCTGGGCGATTCTCCGAAGTGC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGG-CTTTGGGTAATGTTGCTGG-CGATTCTCCGAAGTGC

EST: gi|18963326|gb|BM660372.1|BM660372

EST:     CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAG                         GCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC
genomic: CTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGAC

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: 48 (upstream exon), 48 (downstream exon)
Score: 751

TTCTGGCACTTCAGAAAATACAAAGGCTGTTATTGACCATGGGGCTGTTCCTATATTTGTGAAGCTTCTTGGGTCTGGTAGTGATGATGTTCGTGAGCAGgtatttattc ... caattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 260

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 244

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 430

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taggagtgtgtgatgtgacagtaatgcattttctctgttttaaaacaattaaaagGCTGTGTGGGCTTTGGGTAATGTTGCTGGCGATTCTCCGAAGTGCCGCGACCTTGTTCTCGCCAATGGTGCGTTGATGCCTCTGCTAGCCCAGTTGAATG