ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaaatatatgtttagatcccaattatgcatatgaggtcaaagagataaatgtctaatgttccgactggatatcaatatgcttgtttgttttactcatccag

Basic information

species	Zea mays
transcript	GRMZM2G165817_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G165817_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g10640.1 (Oryza sativa), 5'ss of exon 4

AGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa----atatatgtttagatccc-aattatgcat-----------atgaggtcaaagagataaatgtcta-atgttccgact--ggatatcaatatgcttgtttgttttactcatc-cag
 ||||||||||||||||||||||||||||||||||||||||| || || ||  | ||||| ||||| ||||||||||| || || || ||||| || ||||||||  | |    || | |  ||||||||| |||  |||||           ||||| ||| ||||| | || | |  || || | |||  |||  | | |||  ||   |  |||||||||  |||
TGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGTCCATCGAATTGCCCTTAATGAACCCTGAGCTCTTTCTTCGTGTTGGGATCAAGCCCCCCAAGgtaaatcctacattatttgtacttagatccctaatagtgcatgtaatgtgactatgagatcacagagacatatatatggatattgcaactatggaagttattatattt---tactttactcattgcag

upper sequence: GRMZM2G165817_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S91_182V6.1 (Physcomitrella patens), 5'ss of exon 4

AGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaaatatatgtt-tagatcccaattatgcatatgaggtcaaagagataaat-gtctaatgttccgactggatatcaatatgcttgtttgttttactcatccag
 || || ||   |||||| ||  |||||||| | ||||| |||||||| || ||||||||||| || ||||| || || || || ||||||||||| |||||       |  || |||     ||    | |  |  || |  ||||   |     || | |     ||||   |||  |    ||  ||      | ||||        
TGGAGGACTCAGTGATCAAATCCGAGAGCTCCGTGAGTCAATTGAGTTGCCGCTTATGAATCCCGAGCTCTTCCTGCGAGTTGGCATTAAGCCTCCAAAGgtgtgttttaccatctgtcactaatttagactcagtttacgtagtcatctactcctattgacatgcattcc---tggcgactggtac-ctccacgatattacat------

upper sequence: GRMZM2G165817_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 4

AGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaaatatatgtttagatcccaattatgcatatgaggtcaaagagataaatgtctaatgttccgactggatatcaatatgcttgtttgttttactcatccag
 || || ||   ||| || ||| |||| ||  | ||||| |||||||| ||  | |||||||||||||||||||| || || || ||||| ||||| ||||||  |||  | |  |  ||     |   ||          ||||    || | | ||| || | ||| |||| ||  | |   | | || || ||| | |       
TGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCGATTGAGTTGCCGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgtattcactgacacttactttcgatcagcttccttggccttggtctcc-agtttactgtttattattc-gactcgaagttacccttcgtgattatttgaata------

upper sequence: GRMZM2G165817_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S13_419V6.1 (Physcomitrella patens), 5'ss of exon 4

AGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaaatatatgtttagatcccaattatgcatatgaggtcaaagagataaatgtctaatgttccgactggatatcaatatgcttgtttgttttactcatccag
 || || ||   ||| || ||| |||| ||  | ||||| |||||||| || |||||||| ||||| ||||| ||||| || || ||||||||||| ||||||   |      | |||||   | ||  |     || |  | |  |  |  |    ||   |||   |   ||  |  |  || |        || |   |||    
TGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCAATTGAGTTGCCGCTTATGAACCCTGAGCTCTTCCTTCGAGTTGGCATTAAGCCTCCAAAGgtacctattggcctgtgttttactacc--tcgctgatttt-gatttagcaactgccagtgacatgcatcttttg--tgacgttacgtcctacccttatttccatg---

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|19822398|gb|BQ048422.1|BQ048422

EST:     CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAG
genomic: CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTC-TACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAG

EST: gi|60400478|gb|DN233285.1|DN233285

EST:     CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGG

EST: gi|22472946|gb|BU037426.1|BU037426

EST:     CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGG

EST: gi|15499352|gb|BI595865.1|BI595865

EST:     CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTC
genomic: CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTC

EST: gi|211475160|gb|FL103093.1|FL103093

EST:     CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCAGGAACT-GGAAGACCCTATTGGCAAGG
genomic: CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGG

EST: gi|95107783|gb|EB740012.1|EB740012

EST:     CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGG

EST: gi|148950536|gb|EC896111.2|EC896111

EST:     CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGG

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: 431

AGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCAGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCAAGTAACATCGATGCCAACTTTTTGAAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 354

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 420