ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGGCACCGTGTACATGTTCTCCCTCATCGGCGCCTTCCTCAGCGACTCCTACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgcacacgtctacctacctattaatcgacctgccgatttttccatcgatctgccaatctaccgatcagcagcgtgtgtcggaaagagttttcac...

Basic information

species	Zea mays
transcript	GRMZM2G044851_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G044851_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g46460.1 (Oryza sativa), 5'ss of exon 3

GGGCACCGTGTACATGTTCTCCCTCATCGGCGCCTTCCTCAGCGACTCCTACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgcacacgtctacctacctattaatcgacctgccgatttttccatcgatctgccaatctaccgatcagcagcgtgtgtcggaaagagttt--tcac
 ||||| || ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| |||||   |||    |  |  | |  |   ||   | || | | | ||     | |   |    | |        | ||  ||     | |  | |    ||
CGGCACGGTTTACATGTTCTCCCTCATCGGCGCCTTCCTCAGCGACTCCTACTGGGGCCGCTACAAGACCTGCGCCATATTCCAGGCCATCTTTGTCCTTgtaagcaccaccacacggcacatccctctctc--tccgcagttctatctgaaaaccacgcgcctttctcggtgcgatcgattgatctcatgtttctagctac

upper sequence: GRMZM2G044851_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G49470.1 (Glycine max), 5'ss of exon 4

-GGGCACCGTGTACATGTTCTCCCTCATCGGCGCCTTCCTCAGCGACTCCTACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgcacacgtctacctacctattaatcgacctgccgattttt--ccatcgatctgccaatctaccgatcagcagcgtgtgtcggaaagagttttcac
  || || || ||| | ||||| ||  | || |||||||| || ||||| ||||||||| | |||| |||||| ||||||||||||| ||| |||||  | |||||| |    |       ||| ||  ||       ||     | |    |  |||||  |  |  ||  || |  |   ||||| |       | ||   
CAGGGACAGTTTACCTCTTCTCTCTTCTTGGAGCCTTCCTTAGTGACTCTTACTGGGGAAGGTACATGACCTGTGCCATCTTCCAGGTCATATTTGTTATtgtaagtagttatccatattgtacatacaaaagctatagctagcatctaattaatgatctaactttggactaataaataatatgtgttgtcggatttatt---

upper sequence: GRMZM2G044851_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G49460.1 (Glycine max), 5'ss of exon 2

GGGCACCGTGTACATGTTCTCCCTCATCGGCGCCTTCCTCAGCGACTCCTACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgcacacgtctacctacctattaatcgacctgccgatttttccatcgatctgccaatctaccgatcagcagcgtgtgtcggaaagagttttcac--------
 || || || ||| | ||||| ||  | || |||||||| || ||||| ||||||||| | |||| |||||| ||||||||||||| ||| |||||  | ||||||     |  | ||   |   |  || | |   ||  |  ||  |||   |    |||   ||  ||   ||   ||| |     | ||||   |         
AGGGACAGTTTACCTCTTCTCTCTTCTTGGAGCCTTCCTTAGTGACTCTTACTGGGGAAGGTACATGACCTGTGCCATCTTCCAGGTCATATTTGTTATTgtaagtt----atttttattgaagca--aaacaaaaagc--acattcacatatgttaaacaaaaaacacatacacaatatgtttacaggaaagttgataaaattgatt

upper sequence: GRMZM2G044851_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv15s0021g00330.t01 (Vitis vinifera), 5'ss of exon 3

GGGCACCGTGTACATGTTCTCCCTCATCGGCGCCTTCCTCAGCGACTCCTACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgc---acacgtctacctacctattaatcgacctgccgatttttccat-cgatctgccaatctaccgatcagcagcgtgtgtcggaaagagttttcac
 || || || ||||| ||||| ||  | || ||||| || |||||||| ||||||||  | ||||||||||| |||||||| |||| |||||||||| | ||||||  |     |     |||  |     ||  |    |  ||||  |  ||    |||| |   |||    | | ||  || ||| |||  |         
TGGAACTGTCTACATTTTCTCTCTTCTGGGTGCCTTTCTTAGCGACTCTTACTGGGGGAGGTACAAGACCTGTGCCATCTTTCAGGTCATCTTTGTCATTgtaagtttctaagtataaagaccatcaaggaaaatgtatcgaggattgatttatatagtctgtcttcctagttct-aacaaagtatgttggattgcag------

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|76927974|gb|DV171443.1|DV171443

EST:     ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTC                         GGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC
genomic: ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgca ... gctgctgcagGGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC

EST: gi|148987145|gb|EE030973.2|EE030973

EST:     ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTC                         GGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC
genomic: ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgca ... gctgctgcagGGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC

EST: gi|50328864|gb|CO523990.1|CO523990

EST:     ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTC                         GGCCTCGCGCTGCTGTCGGCGTCGTCGCACCTCTACCTAATCAGGCCGGAC
genomic: ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgca ... gctgctgcagGGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC

EST: gi|86474663|gb|DY241033.1|DY241033

EST:     AGTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTC                         GGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTACTCAGGCCGGAC
genomic: ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgca ... gctgctgcagGGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC

EST: gi|71417415|gb|DR804042.1|DR804042

EST:     ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTC                         GGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC
genomic: ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgca ... gctgctgcagGGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC

EST: gi|74245993|gb|DT653907.1|DT653907

EST:     ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTC                         GGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC
genomic: ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgca ... gctgctgcagGGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC

EST: gi|74237215|gb|DT645129.1|DT645129

EST:     ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTC                         GGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC
genomic: ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgca ... gctgctgcagGGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC

EST: gi|71424538|gb|DR806351.1|DR806351

EST:     ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTC                         GGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC
genomic: ACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgca ... gctgctgcagGGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGAC

EST: gi|74240219|gb|DT648133.1|DT648133

EST:     CTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTTGTCCTC                         GGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGA
genomic: CTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTT-GTCCTCgtaagtcgca ... gctgctgcagGGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGA

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: 35 (upstream exon), 15 (downstream exon)
Score: 1

GGGCACCGTGTACATGTTCTCCCTCATCGGCGCCTTCCTCAGCGACTCCTACTGGGGACGCTACAAGACCTGCGCCATCTTCCAGGCCATCTTTGTCCTCgtaagtcgca ... gctgctgcagGGCCTCGCGCTGCTGTCGGTGTCGTCGCACCTCTACCTAATCAGGCCGGACGGGTGCGGCATGGAGCACGCGCCCTGCGGCCCGCACTCCGGCAAGGAGC

Block sizes: 32 (upstream exon), 22 (downstream exon)
Score: 7

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193