ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTTACAAGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAGgtcctgcacatatattcatttgaatgtatcatagctaacgttcaaggttttcagctactgaatttggatatggaaatttttagttctaaattttttgctt...

Basic information

species	Zea mays
transcript	GRMZM2G164185_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 6

GTTACAAGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAGgtcctgcac-------atatattcatttgaatgtatcatagctaacgttcaaggttttcagctactgaatttggatatggaaatttttagttctaaattttttgctt
|||||||||||||||||||||||| |  |||||||||||||||| | | | ||||||||||||||||||||||| || || |||||||||||||| |  ||       || | || ||||   ||||| |||| ||   ||  |  || |  |||| ||||| ||   | ||  |||   || || ||||   |     
GTTACAAGCCAAGAAACAAGTCTTTCTGCAAGTTGCCGAAGAGTCTTTACGCATGCACATGACTACCATATAAACTCTATTTCAAATAACAGgtcttctacattattaatttttttatttagttgtataatagatattatttgaacttgtt-gctattgaatatgaccacggccatt---agctccaaatgagtgt---

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 6

GTTACAAGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAGgtcctgc---acatatattcatttgaatgtatcatagctaacgttcaa----ggttttcagcta-ctgaatttggatatggaaatttttagttctaaattttttgctt
|| || ||||| || || ||| | |   |  | || || ||||||||||| ||||| ||||| || ||||| ||||| || |||||||||||||  |     || |  |    |   | | ||   |    |  ||  ||    | ||||  | || ||  |||||  |      | | ||  ||  ||| |        
GTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAGgtgatttgaaaccttgagggttcctattttaggctgttcagtgtggaatcttgctttttggttatctttatttgttttaacgtagtgttgatttgaaagt--------

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 6

GTTACAAGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAGgtcctgcacatatattcatttgaatgtatcatagctaacgttcaaggttttcagctactgaatttggatatggaaatttttagttctaaattttttgctt------
|| || ||||| || || ||| |     |  | ||||| ||||||||||| ||||| ||||| || ||||| ||||| || |||||||||||||         |   ||    |    ||| ||||     |||||  ||       | ||   ||||| |||    |||| |  |  |  | | ||   ||      
GTAACCAGCCATGAGACCAGTTTGATGGCTCGATGCCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAGgt--gatttgaaacctcgagggttcctataatagtc--tgttcagtgtcaaatcttgct--ttttggttatctttatttcttttattgtagtgttgatttgaaagt

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 8

GTTACAAGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAGgtcctgcacatatattcatttgaatgtatcatagctaacgttcaaggttttcagctactgaatttggatatggaaattttta-------gttctaaattttttgctt
|| || ||||| ||  | || | ||   | || || |||||||||||||||||||| ||||| || ||||| ||||| || |||||||||||||   |   ||  |  |||| ||||  | | |   |     | |    |  || || ||  |||||       ||| ||  |         | ||| |  | ||   
GTAACTAGCCATGAGTCGAGCCCTGTGGCTAGATGTCGAAGAGTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAGgt--aggttattcacccattggaattcaacttgcttccttctta---ctagcaactgctttatttgtccgcaaaaaattcaatgatgtcactataagtcgtctga--

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 6

GTTACAAGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAGgt---cctgcacatatattcatttgaatgtatcatagctaacgttcaaggttttcagctactgaatttggatatggaaatttttagttctaaattttttgctt
||||| ||||| || || |  ||||   | || ||||||||||| ||||| ||||| ||||| |||||||| ||||| || || |||| |||||   | |   | ||  ||       | ||   ||   | ||  |  |  | |      ||    ||| | | |     |  ||| || |    | |  |   
GTTACCAGCCAGGAGACTAACCTTGTGGCTAGATGCCGAAGAGTGTATGCCCATGCTCATGATTACCATATTAATTCAATCTCCAATAGCAGgtaatcgttttcctaagttttccctcaggttatatgttttactcttgatatctctt-taacacgtttttgctgtctttctccttaatttttccatctcagg--

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 6

GTTACAAGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAGgtcctgcacatatattcatttgaatgtatcatagctaacgttcaaggttttcagctactgaatttggatatggaaatttttagttctaaattttttgctt--
|| |  || || || |||||    |   | || || || ||| | ||||||||||| |||||||| ||||| ||||| || ||||||||||||| |  | || ||||    |||||  |||           ||  | | |||    ||| | || |   | |    || | | |   |  |||  |   |   
GTGATGAGTCATGAGACAAGCTCAGTGGCCAGGTGTCGGAGAATTTATGCTCATGCCCATGACTATCATATCAATTCCATTTCAAATAACAGgtgc-actcacatatcttgttgaacatattcctctactttttgtatgatttgtattacagcatgtcc-tgtttttatatattggcatgtattcctaattgga

upper sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 6

GTTACA-AGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAGgtcctgcacatatattcatttgaatgtatcatagctaacgttcaaggttttcagctactgaatttggatatggaaatttttagttctaaattttttgctt
  |||| ||| | |||||||| ||  |  | || || |||||| ||||||||||||| |||||||| ||||| ||||| || ||||| |||||||        ||  |   | |   | | | |    | |  || ||   | |  | |     ||||  || |       | | |   | |   |    |||
-GTACACAGCAATGAAACAAGCCTATCAGCTAGATGTCGAAGAATATATGCTCATGCTCATGACTATCATATCAATTCCATTTCAAACAACAGgtgaattctttaattggttataggtttttaaatttttatcttgaatcatatttgttgacttatttcaatttcctttcatgttggatttagcatcaaactt

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|31356630|gb|CD440987.1|CD440987

EST:     GTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAG                         TGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAA
genomic: GTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAGgtcctgcaca ... atttcaacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAA

EST: gi|91057148|gb|EB167566.1|EB167566

EST:     GTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAG                         TGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAA
genomic: GTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAGgtcctgcaca ... atttcaacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAA

EST: gi|67032341|gb|CO461090.1|CO461090

EST:     GTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAG                         TGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAA
genomic: GTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAGgtcctgcaca ... atttcaacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAA

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), 45 (downstream exon)
Score: 125

GTTACAAGCCAAGAAACAAGTCTTGCCACAAGTTGCCGAAGAGTATATGCTCATGCACATGACTACCATATAAATTCGATATCAAATAACAGgtcctgcaca ... atttcaacagTGATGGTGAGACATTTATATCAGCTGATGATTTGCGGATAAATCTATGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91