ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcacccccctcgctgtttccctaccttctcttcttccatccgtccgctgatgatttggacccgccttccctgcag

Basic information

species	Zea mays
transcript	GRMZM5G871262_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 5'ss of exon 1

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcacccccctcgctgtttccctaccttctcttcttccatc---cgtccgctgatgatttggacccgccttccctgcag----------------------------
|||||| ||| |||||||||| ||| |||||||  ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||  |      | |     |||||   | |||   | | ||||    | || |||| | |  |    | |  |    |  |                             
CCATGAAGACCCTCTGGCTCGCCGTCTACATCGCCGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCCATGTTCTACTACGAGGGCGACCAGGACAAgtaag-tagtatacatatacatttccactctttcctctatcccattgcgcatctgctgctaaactctcactgaatgttgttgattggatccgtgtgttgttgcttcctgcag

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G43020.1 (Glycine max), 5'ss of exon 1

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcacccccctcgctgtttccctaccttctcttcttcca----tccgtccgct--gatgatttggacccgccttccc-tgcag
|||||| |   ||||||||||  || |||||| | |||||||||||||||||| |||||||||||||||| ||||||| |||||||||||||||||||||||| |          |   |||||          ||||| || |    | |||  | |   ||||  ||     | |||    |||||
CCATGAAGGACCTCTGGCTCGCAGTCTACATCCTCGACGCCGTCCTCGTCTTCTTCGTCATCCCCTTCGCCATGTTCTTCTACGAGGGCGACCAGGACAAgta-cgaggtttttgttattgtttgaaatttgaatcttcgtcaagtgtttcgtgggtttgaatgaaatgtttgtgactttgtgtgcag

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA03G07890.1 (Glycine max), 5'ss of exon 1

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcaccc----ccctcgctgtttccctaccttctcttcttccatccgtccgctgatgatttggacccgccttccctgcag----------------------------------------------------------
|||||| |   ||||||||||   |||||||| | |||||||||||||||||| |||||||||||||||| |||||||||||||| ||||||||||||||||||    |       |  |     |||    |  ||    | ||       |  | |  |||  | ||  |    | |    ||                                                          
CCATGAAGGACCTCTGGCTCGCAATTTACATCCTCGACGCCGTCCTCGTCTTCTTCGTCATCCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtaagtgtatgtggtgctttttaatttttaaaaaatttaagttttgtgattattagatactgaaattgatactttgtgctaatagcatggtaacaaaaaaaatactgaaattgaaaatgtgttgtgattttgggaatgtgcag

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G18160.1 (Glycine max), 5'ss of exon 1

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaa--------cctcacccccctcgctgtttccct---accttctcttcttccatccg-tccgctgatgatttggacccgccttccctgcag
|||||| |   |||||||||| ||| |||||| | ||||| |||||||||||  |||| ||||||||||| ||||||| ||||||||||||||||||||||||           ||    |  ||| || || | |   |   || |   ||  ||    |    |  || ||||   |    ||   |||||
CCATGAAGGACCTCTGGCTCGCCGTCTACATCCTCGACGCTGTCCTCGTCTTTTTCGTTATCCCCTTCGCCATGTTCTTCTACGAGGGCGACCAGGACAAgtacgagttttttttcttttctttcgttggttgcttcaaaatatcaccatttgaatgaaatgttgtattggtttgtggctttgttgtgtgcag

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA01G30400.1 (Glycine max), 5'ss of exon 1

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcacccccctcgctgtttccctaccttctcttcttccatccgtccgctgatgatttggacccgccttccctgcag------------------------
|||||| |   ||||||||||   |||||||| | |||||||||||||||||| |||| |||||||| || |||||||||||||| ||||||||||||||||||    |      |||  ||     ||  ||    | ||   |   |  | |  | ||||       | |   ||| |                         
CCATGAAGGACCTCTGGCTCGCAATTTACATCCTCGACGCCGTCCTCGTCTTCTTCGTTATCCCCTTTGCCATGTTCTACTACGAAGGCGACCAGGACAAgtaagtgtatg----tcgtggtgcttttaatttgatgtttttt-tttttttgtttttaatttttgtaatcatatactgaaattgaacgaaccagacgttggtccg

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 5'ss of exon 1

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgta---acctcacccccctcgctgtttccctaccttctcttcttccatccgtccg----ctgatga---tttggacccgccttccctgcag-----------
|||||| |   || ||||| |   |||| ||||| |||||  | ||||| ||| | |||||||||||||||||||| | ||| || ||||||||||||||||    | ||        |    || || |||  || |    ||  |      ||    |||||||   ||||    |   ||  ||   |           
CCATGAAGGATCTTTGGCTTGCTATTTATATCGTGGACGCTATTCTCGTGTTCTTTGTCATCCCCTTCGCAATGTTTTTCTATGAAGGCGACCAGGACAAgttcgtagcttgatgaaattttagtatctctatgttgtaagttttgagttaatcgaatactgatgacaatttgtgggctttttttctttcgttttttcacag

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 5'ss of exon 1

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcacccccctcgctgtttccctaccttctcttcttccatccgtccgctgatgatttggacccgccttccctgcag--------------------
| |||| |   || ||||| | ||||||||| |||||||| || || |||||| || ||||||||||||| ||||| | ||| || ||||||||||||||||    |    | || || | |||   |   || | ||     ||   |  | || | || |  |   |       ||  |                    
CTATGAAGGATCTTTGGCTTGCCGTTTACATTGTTGACGCTGTGCTTGTCTTCTTCATCATCCCCTTCGCTATGTTTTTCTATGAAGGCGACCAGGACAAgt---ttgtttctccacgatttttttttttttttttttgagttatt-attagttggtaatgtaaagttgttgatgttgtgggcttgtgttttttactgcag

upper sequence: GRMZM5G871262_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 5'ss of exon 1

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgta---acctca---cccccctcgctgtttccctaccttc-tcttcttccatccgtccgctgatgatttggacccgccttccctgcag-------------
| ||||||   || ||||||| | ||||||| ||||| || || ||||| ||| | || || |||||||| |||||||||||||| ||||||||||||||||    || | |      |  |   | || |      ||| | ||  ||| |  ||  |  | ||||| |   | ||    |     |             
CGATGAGGGATCTGTGGCTCGCCATTTACATTGTTGATGCTGTACTCGTATTCTTTGTTATTCCCTTCGCCATGTTCTACTACGAAGGCGACCAGGACAAgtcggtactttagggtttctattaatattgctgagatttcgtatttctccttttgttaga-gttgattggttgctgcgagactgaaggaaaataaaataaa

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|149015378|gb|EE045218.2|EE045218

EST:     TTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAA                         GTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGC
genomic: TTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcac ... ttccctgcagGTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGC

EST: gi|211082082|gb|FL165096.1|FL165096

EST:     TTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAA                         GTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGC
genomic: TTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcac ... ttccctgcagGTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGC

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: 46 (upstream exon), 48 (downstream exon)
Score: 123

CCATGAGGACGCTCTGGCTCGTCGTTTACATCGTTGACGCCGTCCTCGTCTTCCTCGTCATCCCCTTCGCAATGTTCTACTACGAGGGCGACCAGGACAAgtaacctcac ... ttccctgcagGTCCGTCGGGAAGAGGCTCAGGACCGCGCTCATCTGGGTCGTCGCGTCCGCGGTAGTGTGCGGCCTCGTCCTCGGCATCCTATACG

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 126

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 142