ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AAGCTTAAACAACTCTTTGGACGTGAAAGTCTTACCGCTCATGGTGTCTCGGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttaccggactttctcttggcaaacgtttcccttcctagtcgcgcttgttggagaatttcagtcgtctgccttttggccctgctttgccctctgtt...

Basic information

species	Zea mays
transcript	GRMZM2G332809_T01
intron #	11
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G332809_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os08g39310.1 (Oryza sativa), 5'ss of exon 5

-AAGCTTAAACAACTCTTTGGACGTGAAAGTCTTACCGCTCATGGTGTCTCGGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttaccggactttctcttggcaaacgtttcccttcctagtcgcgcttgttggagaatttcagtcgtctgccttttggccctgctttgccctctgtt-----
 || |||||||||||||||||| |||||||||| || ||     |||| |||||| ||||| ||| | ||||||| || |||| ||| |||  ||| ||||||||||||        | ||    |||     |   ||   | | || || ||| | |  |   ||  | |  || |     | |||    | |   |||     
AAAACTTAAACAACTCTTTGGATGTGAAAGTCTAACTGCCGTGAGTGTTTCGGAG-TTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt---tcctttcagaacaacatcatgtattgagacttgcactggttagtgtttgctagatgacatccatccctgcttgca--actcctagttagtat

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|166649728|gb|EG261609.1|EG261609

EST:     CTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: CTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

EST: gi|60399213|gb|DN232027.1|DN232027

EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

EST: gi|29945154|gb|CB815496.1|CB815496

EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

EST: gi|211191428|gb|FL472425.1|FL472425

EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

EST: gi|5069895|gb|AI737860.1|AI737860

EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

EST: gi|32839425|gb|CD979106.1|CD979106

EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACAATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

EST: gi|94476039|gb|EB704997.1|EB704997

EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

EST: gi|32836647|gb|CD976325.1|CD976325

EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACAATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

EST: gi|32837676|gb|CD977354.1|CD977354

EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACAATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

EST: gi|5069885|gb|AI737850.1|AI737850

EST:     GGA-GTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

EST: gi|32945118|gb|CF049937.1|CF049937

EST:     GGAG-TTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTG                         GCGATACAATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

EST: gi|211060187|gb|FL170394.1|FL170394

EST:     GGAG-TTGCTTTCAGACCACCTTTACACACAATCTACCAATATCTGACTG                         GCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC
genomic: GGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGC

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), 49 (downstream exon)
Score: 107

AAGCTTAAACAACTCTTTGGACGTGAAAGTCTTACCGCTCATGGTGTCTCGGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttacc ... ttggctgcagGCGATACGATTTTCTGGACTCGGCTGGGCTAACATCCTGGGTAGTAGGCGCTGATGAAAGGACAAGGGATCTGCTCAAATTAAGTGTTGTATTTGTATCC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90