ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGATGGTCTGGATGATGCTGATGGAGCAGAGGACGTTCCTTTTGATGAACTTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACAgtgagtactattttttccctacaacacgtatctttagatctccatgtgttggcaacttggcataactattttgagttccatagttgtgttgccattctac...

Basic information

species	Zea mays
transcript	GRMZM2G145104_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G145104_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g43210.1 (Oryza sativa), 5'ss of exon 2

TGATGGTCTGGATGATGCTGATGGAGCAGAGGACGTTCCTTTTGATGAACTTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACAgtgagtactattttttcc--ctacaacacgtatctttagatctccatgtgttggcaacttggcataactattttg---agttccatagttgtgttg--ccattctac
 |||||| |||||||||| ||||| |||||||| |||||||||||||||||||| || |||||||||||||| ||||||||||||||||| ||||||||||| || | | |  |||||  |  ||  || | |  ||   | |  |    |   ||    | |||  | || |||   |  | | |  || |  ||  ||| |    
AGATGGTTTGGATGATGCAGATGGTGCAGAGGATGTTCCTTTTGATGAACTTGTAGGCATGCAAGGCCCTGTTTTCCACTTGGTTGAGAACGCAATAACAgtaaggattttgctttcctgccccacaacatgttcttgttttttta---atgaacagtacgacattgccatgttgcagaacttcttgcttcttatgggccaat----

upper sequence: GRMZM2G145104_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G11570.1 (Glycine max), 5'ss of exon 2

TGATGGTCTGGATGATGCTGATGGAGCAGAGGACGTTCCTTTTGATGAACTTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACAgtgagt--actattttttccctac--aacacgtatctttagatctccatgtgttggcaacttggcataac-tattttgagttccatagttgtgttgccattctac
 ||||||||||||||||||||||||||||| || ||||| ||||||||||||||||| ||||| || || || || || |||||||| |||||| | ||||| |||  |  |   |     ||   ||   | |  |   ||        | ||   ||  |   | | | ||     || ||  |  || |  |  | |     
CGATGGTCTGGATGATGCTGATGGAGCAGAAGATGTTCCCTTTGATGAACTTGTTGGCATGCAGGGTCCAGTTTTTCATTTGGTTGAAAATGCATTTACAgtaagtctatcaacctgatgttattgaaattgaacttgatgagggaagccttttcaaaagctaaaacagcatacgcacagctcattttttttaataactt-----

upper sequence: GRMZM2G145104_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G33840.1 (Glycine max), 5'ss of exon 2

TGATGGTCTGGATGATGCTGATGGAGCAGAGGACGTTCCTTTTGATGAACTTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACAgtgagt--actattttttccctacaacacgtatctttagatctccatg--tgttggcaacttggcataactattttgagttccatagttgtgttgccattctac
 ||||||||||||||||||||||||||||| || ||||| ||||||||||||||||| ||||| || || || || || |||||||| |||||| | || || |||  |  |   |     ||    |  |    ||        | |  | |||  ||  |   | | |   |  | ||  |  | |||| |    | |    
CGATGGTCTGGATGATGCTGATGGAGCAGAAGATGTTCCCTTTGATGAACTTGTTGGCATGCAGGGTCCAGTTTTTCATTTGGTTGAAAATGCATTTACTgtaagtctatcagcatcgttttattgaatttgaacttgatgtgggaagccttttgaaaagctaaaacagc--ataggcgtagctcatttgtttaataacttc--

upper sequence: GRMZM2G145104_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT4G34100.2 (Arabidopsis thaliana), 5'ss of exon 2

TGATGGTCTGGATGATGCTGATGGAGCAGAGGACGTTCCTTTTGATGAACTTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACAgtgagt-actattttttccctacaaca-cgtatctttagatctccatgtgttggcaacttggca--taactattttgagttccata-gttgtgttgccattctac--
||||||  ||||||| |||||||| ||||| |||||||| |||||||| || ||||| |||||||| || || || || ||||||||||||||  | || || |||   | ||| | |  |    ||  |||| |||  |  || ||||     |  |||  |   |  |  || | |  ||   | | ||||     ||| | |  
TGATGGGTTGGATGACGCTGATGGTGCAGAAGACGTTCCATTTGATGAGCTGGTTGGAATGCAAGGTCCAGTGTTTCATTTGGTTGAGAATGCCTTTACTgtaagttgatgtttctactttttggcaatgtatattttaaattctatgttccttcttcttcactattggcccttattaaatcttcatgatgtgc-ataattttgcag

upper sequence: GRMZM2G145104_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0063g00080.t01 (Vitis vinifera), 5'ss of exon 2

TGATGGTCTGGATGATGCTGATGGAGCAGAGGACGTTCCTTTTGATGAACTTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACAgtgagtac-tattttttccctacaacacgtatctttagatctccatgtgttggcaacttggcataactattttgagttccatagttgtgttgccattctac--
||||||||| |||||||||||||| |||||||| || || |||||||| |||||||| |||||||| ||||| || || |||||||| |||||  | || ||||||   |  || |   || | |    ||| |    ||     | |||||  |  |   |||  | |||     |   || || |||||  |    | |  
TGATGGTCTTGATGATGCTGATGGTGCAGAGGATGTGCCCTTTGATGAGCTTGTTGGCATGCAAGGGCCTGTTTTTCATTTGGTTGAAAATGCTTTTACTgtgagtttatcattctcttctgctattgttatttcctaattatgttctgttgttattt---catctccattgatgatggaatggtggtgttttccccttcctt

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|32943964|gb|CF048783.1|CF048783

EST:     TTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACA                         GTTTTGGCCAGCAATGCTATA
genomic: TTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACAgtgagtacta ... ttttctccagGTTTTGGCCAGCAATGCTATA

EST: gi|32936131|gb|CF040943.1|CF040943

EST:     TTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACA                         GTTTTGGCCAGCAATGCTATATTCCTCATTGTTGTGATCTTTGTTCCATTC
genomic: TTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACAgtgagtacta ... ttttctccagGTTTTGGCCAGCAATGCTATATTCCTCATTGTTGTGATCTTTGTTCCATTC

EST: gi|32936096|gb|CF040908.1|CF040908

EST:     TTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACA                         GTTTTGGCCAGCAATGCTATATTCCTCATTGTTGTGATCTTTGCTCCATCC
genomic: TTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACAgtgagtacta ... ttttctccagGTTTTGGCCAGCAATGCTATATTCCTCATTGTTGTGATCTTTGTTCCATTC

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: 49 (upstream exon), 48 (downstream exon)
Score: 294

TGATGGTCTGGATGATGCTGATGGAGCAGAGGACGTTCCTTTTGATGAACTTGTTGGTATGCAAGGCCCTGTCTTCCACTTGGTTGAGAATGCAATAACAgtgagtacta ... ttttctccagGTTTTGGCCAGCAATGCTATATTCCTCATTGTTGTGATCTTTGTTCCATTCTCATTGGGAAGGATTGTTCTGTACTACCTATCATGGTTTTTCTCTTCGG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 259

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 231