ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatctaaatttctgggcatttttctgtgtatactatttaatttggaactttacttttttgttcaaacaaaccttggattacatttctctgttcta...

Basic information

species	Zea mays
transcript	GRMZM2G025366_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2

TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatctaaatttctgggcatttttctgtgtat-actatttaatttggaacttt---acttttttgttcaaacaaaccttggattacatttctctgttcta
||| ||||| ||||| ||||||||||||||||| ||||| || ||||| |||||||||| ||||||||||||| |||||||||| ||||||||||||||||||||    | | ||  |      | |   | | || ||| | |  ||  | |||||    ||   |||||  |||   |  ||  || | |||   ||| || 
TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctttacttcatacattctatctggagcatcactgtctg-ttcagtactttggagctgccttgtttgaactg-cactgagtttc-tttgcgtgtgct-

upper sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G08920.1 (Glycine max), 5'ss of exon 2

TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatctaaatt-tctgggcatttttctgtgtatactatttaatttggaactttacttttttgttcaaacaaaccttggattacatttctctgttcta
 || |||||  |||  |||||||| ||  ||||||||||||| ||||| ||||||||||  ||||| ||||||||||| || || || |||||||||||||||||||  |  | | | ||  | |  ||||   |    ||| |  |||| |    ||| ||  || |  ||  |     |    |   || | || |   
AGAGGTTGCCACAAGGTATCCTGGAATCAAGTACAATGAAATTATTGTAGACAACTGCTGCATGCAGCTTGTTTCAAAACCGGAGCAGTTTGATGTCATGgtatgtaaatttactatttgatcctgattctcaattatttatctgctttg-attaatacattcatggtgtaattatgggggatcaatgcttgtttgcttcc

upper sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G22640.1 (Glycine max), 5'ss of exon 2

TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatctaaatttctgggcatttttctgtgtatactatttaatt-tggaactttacttttt-tgttcaaacaaaccttggattacatttctctgttcta-
 || |||||| |||| || ||||| ||  |||| || ||||| ||||| || ||||||| |||||| |||||||||||||||||||| |||||||||||||||||| | |  |  |       |  ||   ||     |||  | || || || |||   |  | | || |  ||    |  |   |||   |  ||   || 
AGAGGTTGCTACAAAGTACCCTGGAATAAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacattctattctggtttgctgctgtttatgcacttatgtaattttgtctaatgtatttatgcag---taagcacacacacccttgagttaa

upper sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2

TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatctaaatttctgggcatttttctgtgtatact-atttaatt-tggaactttacttttttgttcaaacaaaccttggattacatttctctgttcta
 || |||||| |||| || ||||| ||  |||| || ||||| ||||| || ||||||| |||||| |||||||||||||||||||| |||||||||||||||||| | |  |  | |      |    ||    || | ||  | || || || ||  ||  | | ||    ||            |    | |    |  
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacatttcaatcctggcttgcagctatttatgcacttatgtaatttgtctaatgtatttgtgcagtaacccccccgccccccgcccccc--

upper sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT4G35260.1 (Arabidopsis thaliana), 5'ss of exon 2

TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatctaaatttctgggcatttttctgtgtatactatttaatttggaactttacttttttgttc---aaacaaaccttggattacatttctctgttcta
 || |||||   ||| |||||  | ||    ||||||||||| |||||||| ||||||| ||||||||||||  | || || || ||||| ||||||||||||||| || | | || |   ||| |   | |  ||    ||   |||    |||   | ||||  |     || ||        | |  | || ||  | | 
CGAGGTTGCGAAAAAGTATCCCAGCATCACCTACAATGAAATCATTGTTGATAACTGCTGTATGCAACTTGTAGCCAAACCAGAGCAATTCGATGTCATGgtatgtttc-agagttatatacatatgaattttcatgacgttc--tttaagtcttcgatgttttactttgagaaaaagataccagtcatctctccctagtttg

upper sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT4G35650.1 (Arabidopsis thaliana), 5'ss of exon 2

TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgta-tgtatctaaatttctgggcatttttctgtgtatactattt---aatttgg----------aactttactt--ttttgttcaaacaaaccttg-gattacatttctctgttcta------
 || ||||||  | | ||| | || |||   ||||||||||| || || ||||| |||| |||||| |||||  | |||||||| |||||||||||||||||| ||    |   || || |  |    ||    |     ||||   ||| ||           |||  |  ||  | |||||   |     ||   |  ||  |||   || | |       
AGAGGTTGCTAAACATTATTCGGGGATTACTTACAATGAAATAATCGTAGACAATTGCTGTATGCAGCTTGTCGCCAAGCCTGAGCAATTTGATGTCATGgtaatgctcttcttttcctagttacaaatcaaaatgagtcattttgaaatgtgacagacgatgaaaccatcattgatgttgttttgatgtctctcatggatattttttgttggtttgtttcag

upper sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 2

TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatctaaatttctgggcatttttctgtgtatactatttaatttggaactttacttttttgttcaaacaaaccttggattacatttctctgttcta----
 ||||||||   ||| || ||  |||||   ||||  ||||| ||||| || |||||||  |||||||| ||||||||||| || |||||||||||||||||||||  ||       |||   | ||||   | | ||  ||  ||   |    | | | |  || |  |  |   ||||   ||  ||| | | |   |    
GGAAGTTGCGAAAAATTACCCCAGTATTGCATACAGCGAAATTATTGTGGATAACTGCTGCATGCAACTGGTTTCAAAGCCGGAGCAATTTGATGTCATGgtatgtggctttgcaaatggatttatttcatgggaaacctttctat--agccactaattctgctgat--attattacttgatatatgtttgtatctataaactg

upper sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 2

TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatctaaatttctg---ggcatttttctgtgtatactatttaatttggaactttacttttttgttcaaacaaaccttggattacatttctctgttcta
 || |||||  ||||||||||||| ||  |||||| |||||| ||||| ||||| ||||  ||||| ||||||||||||||||| || ||||||||||||||||||   || | |  ||    ||| |||  |    || | | ||  || |  | | |  | |  |||||     ||   |   | | |||||    |   |
AGAGGTTGCAACAAAATATCCTGGAATCAAGTACAGTGAAATTATTGTGGACAATTGCTGCATGCAGCTTGTTTCAAAGCCTGAGCAGTTTGATGTCATGgtatgtgaatatactattgtatagcactttaattgagatgcaaattgcttggtcaatgt-ttgtcatgttctgt--aattattcttaagatttcctgatagca

upper sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2

TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatctaaatttctggg-catttttctgtgtatactatttaat--------------ttggaactttacttttttgt----tcaaacaaaccttggattacatttctctgttcta---------------------------
||| || ||   ||| ||||| |  ||  |||| || ||  | ||||| || || |||| |||||| ||||| || |||||| |||||||||||||||||||| ||      || || ||  || ||||||  |  |  || ||| |              |    |||| |  ||  |||    |||     | ||  ||||  | || | ||   |                            
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag

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|149089013|gb|EE178164.2|EE178164

EST:     NCA-CTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATG                         GTTACGCCTAATCTTTATGGCCATTTTGGTGGCTAACACGGCTGCAGGTAT
genomic: -CAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatct ... ttttttgtagGTTACGCCTAATCTTTATGGCAATTT-GGTGGCTAACACGGCTGCAGGTAT

EST: gi|148959186|gb|EE010640.2|EE010640

EST:     ACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATG                         GTTACGCCTAATCTTTATGGCAATTTGGGGGCTAACACGGCTGCAGGTATT
genomic: ACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatct ... ttttttgtagGTTACGCCTAATCTTTATGGCAATTTGGTGGCTAACACGGCTGCAGGTATT

EST: gi|148959185|gb|EC905302.2|EC905302

EST:     ACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATG                         GTTACGCCTAATCTTTA
genomic: ACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatct ... ttttttgtagGTTACGCCTAATCTTTA

EST: gi|5901228|gb|AW042328.1|AW042328

EST:     AACTGCTCTATGCAACTTGTTTCAAAGGCCTGAACAATTTGATGGTCATG                         GTTACGCCTAATCTTTATGGCAATTTG
genomic: AACTGCTCTATGCAACTTGTTTCAAAG-CCTGAACAATTTGATG-TCATGgtatgtatct ... ttttttgtagGTTACGCCTAATCTTTATGGCAATTTG

EST: gi|76285692|gb|DV025260.1|DV025260

EST:     ACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATG                         GTTACGCCTAATCTTTATGGCAATTTGGTGGCTAACACGGCTGCAGGTATT
genomic: ACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatct ... ttttttgtagGTTACGCCTAATCTTTATGGCAATTTGGTGGCTAACACGGCTGCAGGTATT

EST: gi|76285693|gb|DV025261.1|DV025261

EST:     ACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATG                         GTTACGCCTAATCTTTATGGCANTTTGGTGGCTAACACGGCTGCA
genomic: ACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatct ... ttttttgtagGTTACGCCTAATCTTTATGGCAATTTGGTGGCTAACACGGCTGCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 48

TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatct ... ttttttgtagGTTACGCCTAATCTTTATGGCAATTTGGTGGCTAACACGGCTGCAGGTATTGTTGGAGGGACGGGCATCATGCCTGGAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84