ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatcttttggcctagaatcacacgttcacacttgagcaccgtttttagcttttgtttaccgtcttgcagtgtcatcccttctttcaaaacctagctga...

Basic information

species	Zea mays
transcript	GRMZM2G139683_T03
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g07020.2 (Oryza sativa), 5'ss of exon 3

GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatcttttgg--cctagaatcacacgttcacacttgagcaccgttt-ttagcttttgtttaccgtcttgcagtgtcatcccttctttcaaaacctagctga--
|||||||||||||||||||||||||||||| ||||||||||| |||||||| |||||||||||||||||| ||| |||||||||| ||||   ||     ||  |   | |||| ||  |||| ||| | | | ||| | ||      | |  |  ||||| |||    ||  || |  | |  
GTATCCACACTGCCTTTTCTTTCTTGAGCTCCTCCAAAATGCGAATTTCCGGAATGCAATGGCACATCCAGCAAGCAAGgtgatcctttgaatccctttttcctagaattacacatg--caccatttgtcaacctttttatagtactgttctataacatcctttca---aattcccattttatt

upper sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g41450.1 (Oryza sativa), 5'ss of exon 4

GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatcttttggcctagaatcacacgttcacacttgagcaccgtttttagcttttgtt-taccgtcttgcagtgtcatccc---ttctttcaaaacctagctga
|||||| ||||||||||||||||||||||| ||||||||||| |||||||| ||||||||||| |||||| ||| |||||||| | ||||    |           |   ||    |  || |||  | ||||| |  ||||| ||   |   || |  |   ||    |   |   ||   |
GTATCCGCACTGCCTTTTCTTTCTTGAGCTCCTCCAAAATGCGAATTTCCGGAATGCAATGGCCCATCCAGCAAGCAAGgtgaccctttga---aaccctttttcctagtacacatgtgccatttcaaccttttatagtaccgcct-ataacatcctttcagatttcccctttattaagtgta

upper sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G28990.1 (Glycine max), 5'ss of exon 4

GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatcttttg-gcctagaatcacacgttcacacttg-agcaccgtttttagcttttgttt---accgtcttgcagtgtcatcccttctttcaaaacctagctga
|||||| || ||||| |  ||||||||||| || || ||||| ||||| || || ||||||||||||||||| || ||||| |      |   ||     | |  ||    | |    |||   | | |  ||||| |     |   || |  | |  ||    | |||  |||   ||     
GTATCCTCATTGCCTCTATTTTCTTGAGCTGCTTCAGAATGCAAATTTTCGCAACGCAATGGCACATCCAACCAATAAGgtaaatggcagtatctttttgctcctgtctgaagtaacggcattctctatttcttttataatagattctcctttaatagcaaatttgcttgtaaa-tgtat----

upper sequence: GRMZM2G139683_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G38750.2 (Glycine max), 5'ss of exon 5

GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatcttttggcctagaatcacacgttcacacttgagcaccgtttttagcttttgtttaccgtcttgcagtgtcatcccttctttcaaaacctagctga--------
|||||| || ||||| |  ||||||||||| || || ||||| ||||| || ||||||||||| |||||||| || ||||| |    |||   ||   |    | | |   ||  || | ||   |||   | | |||    | |   ||  |  ||| ||  |   |||  ||  ||         
GTATCCTCATTGCCTCTATTTTCTTGAGCTGCTTCAGAATGCAAATTTTCGCAATGCAATGGCGCATCCAACCAATAAGgtaa---attgcagtatctttttgc-tcctgtctgaagtaacggcctta---tctatttcttttataatag-attctcctttaatatcaaatttacttgtaattgtat

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|76934686|gb|DV173976.1|DV173976

EST:     TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAG                         GAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC
genomic: TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatctttt ... tgtttgacagGAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC

EST: gi|28910217|gb|CB331329.1|CB331329

EST:     TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAG                         GAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC
genomic: TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatctttt ... tgtttgacagGAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC

EST: gi|26559121|gb|CA831356.1|CA831356

EST:     TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAG                         GAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC
genomic: TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatctttt ... tgtttgacagGAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC

EST: gi|87157028|gb|DY401817.1|DY401817

EST:     TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAG                         GAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC
genomic: TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatctttt ... tgtttgacagGAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC

EST: gi|22521504|gb|BU080315.1|BU080315

EST:     TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAG                         GAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC
genomic: TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatctttt ... tgtttgacagGAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC

EST: gi|60352751|gb|DN219724.1|DN219724

EST:     TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAG                         GAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC
genomic: TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatctttt ... tgtttgacagGAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC

EST: gi|71765862|gb|DR963799.1|DR963799

EST:     TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAG                         GAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC
genomic: TTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatctttt ... tgtttgacagGAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAAC

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), 47 (downstream exon)
Score: 37

GTATCCACACTGCCTTTTCTTTCTTGAGCTTCTCCAAAATGCCAATTTCCGAAATGCAATGGCACATCCAACAAACAAGgtgatctttt ... tgtttgacagGAGCTTGCTCATAGGCAGCAATATTTCTTCTGGAAAAACTACAGGAATAACAGACTGAAGCACATCATACCGCGCCCTCCTCCTGAACCTGCACCTTCAC

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 64

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 92