ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TATTATACTCATTAGAGATATTCCTGATGCGAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAGgtaatcaactaatcattctgcaggcatgtaatttggaaatccgttgtaagatactgatttaatttcattttttgtctaaatgtttttttcttttgtttct...

Basic information

species	Zea mays
transcript	GRMZM2G178618_T01
intron #	10
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 5'ss of exon 10

TATTATACTCATTAGAGATATTCCTGATGCGAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAGgtaat---caactaatcattctgcaggcatgtaatttggaaatccgttgtaagatactgatttaatttcattttttgtctaaatgtttttttcttttgtttct
||| |||||||||||||||||||||||||| || ||||| |||||||||||||| || |||||||| ||||| ||||| ||||| ||| |||| |||||||||||   |||   |||||| |  |    |||| |||| || ||  | || |  | |  | |||       || |    ||| ||      | |  || ||  
TATCATACTCATTAGAGATATTCCTGATGCAAAAGAAAGTGGTTTATTTCACTTGTGTGAATTCATTGAAGATTGTGAGTTCACTTATATGTCTACTCAGgtaatggccaatctatcattttataaatgtgtattttgcaagtcactagttatttccgaacttagga--ggttgtaacttaattgcgacaatgtcatgcttg-

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA04G01470.1 (Glycine max), 5'ss of exon 10

TATTATACTCATTAGAGATATTCCTGATGCGAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAGgtaatcaactaatcattctgcaggcatgtaatttggaaatccgttgtaagatactgatttaatttc--attttttgtctaaatgtttttttcttttgtttct------------
| | || |||||||||||||| ||| |||| ||||||   || ||  ||||  | || || ||||||||||| ||||| ||||| ||||||||||| |||||| |  |||    | |      || |||  ||    | ||  |  |     | |  |||  | |   ||| |   |||   |  ||     ||||||| |             
TGTGATTCTCATTAGAGATATCCCTAATGCAAAGGAAGCTGGGTTGCTTCATCTTTGTGAGTTCATAGAAGATTGTGAGTTCACTTATTTGTCCACACAGgtatt--acttccgactt---gtgcttgtgcttcattattcactgtttgtgcatttcttttgtctggaattctacatcttggttgttaacgattttgttccccttgtactgtag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA11G12610.1 (Glycine max), 5'ss of exon 10

TATTATACTCATTAGAGATATTCCTGATGCGAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAGgtaatcaactaatcattctgcaggcatgtaatttggaaatccgttgtaagatactgatttaatttcattttttgtctaaatgtttttttcttttgtttct
| | || || ||||||||||| |||||||| |||||||| || ||  ||||| | || || || || ||||| ||||||||||| ||||||||||| |||||| | |  |     || | |     ||  ||||       | ||||  | | |||  |   ||| || |||||    ||| ||| | ||| |   ||  
TGTGATTCTTATTAGAGATATCCCTGATGCTAAGGAAAGTGGGTTGCTTCACCTTTGTGAGTTTATTGAAGATTGTGAATTCACTTATTTGTCCACACAGgtagtaattttggttttgtcc---tttgccattta------ctttgtgtgcttctggat---ttttatcttttggt--aatttttctctctatcccttag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 5'ss of exon 10

TATTATACTCATTAGAGATATTCCTGATGCGAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAGgtaatcaactaatcattctgcaggcatgtaatttggaaatccgttgta-agatactgatttaatttcattttttgtctaaatgtttttttcttttgtttct
  | || ||||| ||||||||||||||||| || |||||||| ||  ||||  | || ||||| || ||||| ||||| ||||||||| | || || ||||||      |  ||  | |  |    | |||||         | |||  |  ||||  ||| | |  |  |  | |    |  ||| |||| ||  ||   
CGTGATCCTCATAAGAGATATTCCTGATGCAAAAGAAAGCGGGTTGCTTCATCTGTGTGAATTTATTGAAGATTGTGAGTTCACCTATCTTTCAACACAGgtagcatttttctccattta-atatctttaattcaagctcatggtgtttatttacttctttgactatagatagtctactcaattttatttccttaattcag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S276_96V6.1 (Physcomitrella patens), 5'ss of exon 10

TATTATACTCATTAGAGATATTCCTGATGCGAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAGgtaatcaactaatcattctgcaggcatgtaatt-tggaaatccgttgtaagatac-tgatttaatttcattttttg---tctaaatgtttttttcttttgtttct---------------------------------------------------------------------------------
| | || |||||  | || ||||||||||| |||||||||||  | | |||| | ||||| ||||||||||| || |||||||||||  |||| || ||||| |  ||  | |   | |   |   ||      |  |  ||| |  ||   ||| |  |  ||     || |       |     |||||||  |||| ||  |                                                                                 
TCTCATCCTCATCCGTGAGATTCCTGATGCTAAGGAAAGCGGACTGTCTCACCTTTGCGAGTTCATAGAAGATTGCGAATTCACCTACCTGTCTACGCAGgttagtaatcactgcgtgttgtgttgtgcggcagtacacttccatgatattttaccttgtacaacggtgttgtagagaaccctctggttttttctttttattaatagaaatgacgactttgccggaacactaaaacatcagtccagcgtgagaaagtcatattttactaaccctttttgattgcag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S41_154V6.1 (Physcomitrella patens), 5'ss of exon 10

TATTATACTCATTAGAGATATTCCTGATGCGAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAGgtaatcaactaatcattctgcaggcatgtaatttggaaatccgttgtaagatactgatttaatttcattttttgtctaaatgtttttttcttttgtttct--------
  |||| |||||| | || |||||||| || |||||||| ||  | | |||  | |||||||||||||||||||| |||||||||||  |||| |||||||| | |||  | | |||     |   || |||        || |   |||    |  | | | || |||| |||  | |  |    ||| || |  |  |        
ACTTATCCTCATTCGTGAGATTCCTGACGCTAAGGAAAGTGGACTCTCTCATCTCTGCGAATTCATAGAAGACTGCGAATTCACCTACCTGTCTACTCAGgttagcaatcactgatt-----gctgtgaaatcc---ctcccatccgaaggagattgtctcaattgatttcttgagttagagacagtttattataataataacacttt

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|18654639|gb|BM499444.1|BM499444

EST:     CTTATGCGAATTCATAGAAGCACTGTGAATTCACCTATTTGTCCACTCAG                         AT-CTTC-CTTTTTGGGAAATGAAGGCCCCAAAACATCAGATCCCAGTAAA
genomic: CTTATGCGAATTCATAGAAG-ACTGTGAATTCACCTATTTGTCCACTCAGgtaatcaact ... cttgtggcagATACTTCACTTTTTGGGAAATGAAGGCCCCAAAACATCAGATCCCAGTAAA

EST: gi|18648972|gb|BM497791.1|BM497791

EST:     ACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAG                         ATACTTCACTTTTTGGGAAATGAAGGCCCCAAAACATCAGATCCCAGTAAA
genomic: ACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAGgtaatcaact ... cttgtggcagATACTTCACTTTTTGGGAAATGAAGGCCCCAAAACATCAGATCCCAGTAAA

EST: gi|18654638|gb|BM499443.1|BM499443

EST:     ACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCC-CTCAG                         AT-CTTC-CTTTTTGGGAAATGAAGGCCCCAAAACATCAGATCC
genomic: ACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAGgtaatcaact ... cttgtggcagATACTTCACTTTTTGGGAAATGAAGGCCCCAAAACATCAGATCC

EST: gi|6564183|gb|AW231805.1|AW231805

EST:     ACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAG                         ATACTTCACTTTTTGGGAAATGAAGGCCCCAAAACATCAGATCCCAGTAAA
genomic: ACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAGgtaatcaact ... cttgtggcagATACTTCACTTTTTGGGAAATGAAGGCCCCAAAACATCAGATCCCAGTAAA

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), 49 (downstream exon)
Score: 269

TATTATACTCATTAGAGATATTCCTGATGCGAAGGAAAGCGGTTTATTTCACTTATGCGAATTCATAGAAGACTGTGAATTCACCTATTTGTCCACTCAGgtaatcaact ... cttgtggcagATACTTCACTTTTTGGGAAATGAAGGCCCCAAAACATCAGATCCCAGTAAATACATACGCTATATATACAATAGGGTGATACTTGAAAATGCTACAGTTC

Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 201

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 186