ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtattgcccccacaatccgttatgtcacccggtcctcccgcacctttcttttttttcgttgcacggctgcctcacagttagtgcacaagtaaaataaaaggcaagtggccctttattttgggtgcactcctaccggtagtgcatgttaagctcacaactacatctgttgctgtttacattggcaccagGTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCCCCTTTGGCGGCGGCTGTGACGCACGCGAATGTCCGGGTAGGTAGCAGGA

Basic information

species	Zea mays
transcript	GRMZM2G044866_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G044866_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g45490.1 (Oryza sativa), 3'ss of exon 8

gtattgcccccacaatccgttatgtcacccggtcctcccgcacctttcttttttttcgttgcacggctgcctcacagttagtgcacaagtaaaataaaaggcaagtggccctttattttgggtgcactcctaccggtagtgcatgtt---------aagctcacaactacatctgtt---gctgtttacattggcaccagGTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCCCCTTTGGCGGCGGCTGTGACGCACGCGAATGTCCGGGTAGGTAGCAGGA
               |   | ||   ||    |  |        |  | |  ||       |||     |     |  ||     ||    || ||||   | |||| |||| |||||   |||   |||||  || ||  ||||||         ||||| || | |  |||||||   |||||||    |  ||||||| |||||||||||||||||| ||||| ||||||||||| ||| ||| |||||||    ||||   ||   |       ||  || |  ||||||||||||
--------------gtttctcatcctactacataatttttgttttcacatacttcctaggacacaagcacacactacctaacctgcag---aactaaactaccagtg-ccctgtatttcctgtg---tcctattggcagcacatgttgaacctcataagcttactagtgtatctgtttttgctgtttgacatcacaccagGGATACCACAGGGAGCTACTAGAGCAAATGATTGCATCCGGTTGGAAGCCCCCTCCAACGGCCAGTGAACCATCTCGAAAACTCAGATTAGGTAGCAGGA

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|32936542|gb|CF041361.1|CF041361

EST:     GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAG                         GTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC
genomic: GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAGgtattgcccc ... ttggcaccagGTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC

EST: gi|71313493|gb|DR793305.1|DR793305

EST:     GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAG                         GTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC
genomic: GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAGgtattgcccc ... ttggcaccagGTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC

EST: gi|32936757|gb|CF041576.1|CF041576

EST:     GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAG                         GTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC
genomic: GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAGgtattgcccc ... ttggcaccagGTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC

EST: gi|83278829|gb|DV942837.1|DV942837

EST:     GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAG                         GTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC
genomic: GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAGgtattgcccc ... ttggcaccagGTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC

EST: gi|4647294|gb|AI622369.1|AI622369

EST:     GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAG                         GTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC
genomic: GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAGgtattgcccc ... ttggcaccagGTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC

EST: gi|32936590|gb|CF041409.1|CF041409

EST:     GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAG                         GTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGAATGCCC
genomic: GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAGgtattgcccc ... ttggcaccagGTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC

EST: gi|32936641|gb|CF041460.1|CF041460

EST:     GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAG                         GTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC
genomic: GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAGgtattgcccc ... ttggcaccagGTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC

EST: gi|32936797|gb|CF041616.1|CF041616

EST:     GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAG                         GTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC
genomic: GGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAGgtattgcccc ... ttggcaccagGTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCC

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: 39 (upstream exon), 22 (downstream exon)
Score: 2

CCAGATCAGTTTCAGCACGGTCCGGGACAAAATCAGGGCTAGAGTTGGCTGGATGCCTGAGATGTTCATGGACTGCGAAAGGCGCAACTTTGTCGTTCAGgtattgcccc ... ttggcaccagGTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCCCCTTTGGCGGCGGCTGTGACGCACGCGAATGTCCGGGTAGGTAGCAGGA

Block sizes: 44 (upstream exon), 37 (downstream exon)
Score: 4

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 13

Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 7

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cggtagtgcatgttaagctcacaactacatctgttgctgtttacattggcaccagGTATACCACAGGGAGCTACTGGAGCAGATGATTGCATCTGGTAGGATGCCCCCTTTGGCGGCGGCTGTGACGCACGCGAATGTCCGGGTAGGTAGCAGGA