ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGAGCTGATTGCCACGAACTGGCCTTACTGGAACAGATCAGAGGGTGCAGATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAGgtacaaacaccaccggtacatgaagtagctgtagcgtgcatttatctatgcttccattaataaagtttagatgctaatcaataatagatgagtattgaat...

Basic information

species	Zea mays
transcript	GRMZM2G000581_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G000581_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 5'ss of exon 2

TGAGCTGATTGCCACGAACTGGCCTTACTGGAACAGATCAGAGGGTGCAGATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAGgtacaaacaccaccggtacatgaagtagctgtagcgtgcatttatctatgcttccattaataaagtttagatgctaatcaataatagatgagtattgaat------
|||||||||||| || || |||||||||||||| ||||||||||| || |||||||||||||| || |||||||||||||| ||||||||||| |||||||||||  ||| |   |||||  |  | ||||| |    |||||||   | |||   | |  ||| | | ||   | | || || |   | |||| ||||       
TGAGCTGATTGCAACAAATTGGCCTTACTGGAATAGATCAGAGGGGGCTGATCATTTCTTTGTTACACCACATGACTTTGGCGCTTGCTTCCACTATCAGgtacatgcacaa---gtacaaaaccttgctgttggacacatttattcctcctttagtgagcaaattctggactttgagcattagt---ttagtactgaacacttaa

upper sequence: GRMZM2G000581_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA05G33420.1 (Glycine max), 5'ss of exon 2

TGAGCTGATTGCCACGAACTGGCCTTACTGGAACAGATCAGAGGGTGCAGATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAGgtacaa----------acaccaccggta-catgaagtagctgtagcgtgcatttatcta-tgcttccattaataa-----------agtttagatgctaatcaataatagatgagtattgaat-------------------------------
  |||| ||| |  | ||||||||||| |||||| |  ||||||| || ||||| ||||||||    || ||||||||||| || || |||||||| |||||||||          | | ||| | ||   | |  ||  | |      || |||| |  ||  |  |  | |||           ||||||||||      |   ||  |  ||||    ||                               
ACAGCTTATTTCTTCAAACTGGCCTTATTGGAACCGGACAGAGGGGGCTGATCACTTCTTTGTGGTTCCTCATGACTTTGGGGCATGTTTCCATTACCAGgtacaagatttttcacatatcactgttagttttacttaagtatttgaaccaattatatgctgtcttgagaagtaacaaagaaaagcagtttagatgtaggatacctatccaaaagtaacacataacatgcattttattcattattttgttctag

upper sequence: GRMZM2G000581_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA04G37920.1 (Glycine max), 5'ss of exon 2

TGAGCTGATTGCCACGAACTGGCCTTACTGGAACAGATCAGAGGGTGCAGATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAGgtacaaacaccaccggtacatgaagtagctgtagcgtgcatttatctatgcttccattaataaagtttagatgctaatcaataatagatgagta-----ttgaat---------------------------------------------------------------
  |||| ||| |  | ||||||||||| ||||||||  |||| || ||||||||||||||||| || || ||||||||||| || |||||||||||||| |||  ||    |  |   | |        ||     | |||  |    |  ||| ||||| ||     | |   |      |  | | |||| |     ||| ||                                                               
ACAGCTTATTTCTTCAAACTGGCCTTATTGGAACAGGACAGAAGGGGCAGATCATTTCTTTGTGACCCCTCATGACTTTGGGGCATGCTTCCATTATCAAgtaagaaatttagtgtaccgttttaattttgctattttcatc-actattagttctattaagaattcaaacaaattgtgtggtgtttggtgagaaggaccttggattttattcttcaatatgtacatggatattgtaacatgcacttttatcatgtttttccgttccag

upper sequence: GRMZM2G000581_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA06G17140.1 (Glycine max), 5'ss of exon 2

TGAGCTGATTGCCACGAACTGGCCTTACTGGAACAGATCAGAGGGTGCAGATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAGgtacaaacaccaccggtacatgaagtagctgtagcgtgcatt--tatctatgcttccattaat----aaagtttagatgctaatcaataatagatgagtattgaat--------------------------------------------------------------
  |||| ||| |  | ||||||||||| ||||||||  |||| || ||||||||||||||||| || || ||||||||||| || |||||||||||||| |||  ||    |  |   |||        |||    |  ||   |||   | |||  |  |||    | |  ||   || |  |   | | | | ||  || || |                                                              
ACAGCTTATTTCTTCAAACTGGCCTTATTGGAACAGGACAGAAGGGGCAGATCATTTCTTTGTGACCCCTCATGACTTTGGGGCATGCTTCCATTATCAAgtaagaaatttagtgtaccattttaattttgttatttaaatcactattagttcttttaagaattcaaacaaattttgtggtttttggtgaca-aggaccatggattccactattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccag

upper sequence: GRMZM2G000581_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G27440.1 (Arabidopsis thaliana), 5'ss of exon 2

TGAGCTGATTGCCACGAACTGGCCTTACTGGAACAGATCAGAGGGTGCAGATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAGgtacaaacaccaccg-gtacatgaagtagctgtagcgtgcatttatctatgcttccattaataaagtt-tagatgctaatcaataatag---atgagtattgaat--
  | || ||  |  | || |||||||| |||||  |  | || || || ||||| ||||||||   ||| ||||||||||| |||||||||||||||||||||  |  | | | |  | || |||  | || ||       ||| | ||||| |  | || |   ||  | | || | ||||| ||||     |||   |  |||  
ACAACTAATCTCATCAAATTGGCCTTATTGGAATCGGACTGAAGGAGCTGATCACTTCTTTGTTGTGCCCCATGACTTTGGAGCTTGCTTCCATTATCAGgta-gattatctctgcattcaggaacaaactctat------tttttatatgcattgaatactttggtggttgctgttcatcaagaataccctgtgatcttacaatga

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|71445197|gb|DR826247.1|DR826247

EST:     ATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAG                         GAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAGCGTGCTACA
genomic: ATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAGgtacaaacac ... ttattttcagGAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAGCGTGCTACA

EST: gi|76911648|gb|DV164366.1|DV164366

EST:     ATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAG                         GAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAGCGTGCTACA
genomic: ATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAGgtacaaacac ... ttattttcagGAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAGCGTGCTACA

EST: gi|67014904|gb|CO443653.1|CO443653

EST:     ATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAG                         GAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAGCGTGCTACA
genomic: ATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAGgtacaaacac ... ttattttcagGAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAGCGTGCTACA

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: 43 (upstream exon), 44 (downstream exon)
Score: 24

TGAGCTGATTGCCACGAACTGGCCTTACTGGAACAGATCAGAGGGTGCAGATCATTTCTTTGTCACGCCACATGACTTTGGTGCTTGCTTCCATTATCAGgtacaaacac ... ttattttcagGAAGAGAAAGCAATCGGGCGGGGAATCCTTCCCTTGCTTCAGCGTGCTACACTGGTTCAGACCTTTGGACAGAAGAACCATGTCTGCCTGAAGGGCGGGT

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 26

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 63