ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaattcatgttcatgacatacagaagtgtctgttcatctaaaggggaactaatgatgccagtgatatttatcag

Basic information

species	Zea mays
transcript	GRMZM2G013079_T01
intron #	9
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G013079_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9

ACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaattcatgttcatgacatacagaagtgtctgttcatctaaaggggaactaatgatgccagtgatattt-atcag
|||||||||||||||||||||| || ||||||||||||||||| || ||||||||||| || ||||| ||||| ||||| || || ||||||||||||||||||||||     |||  |||| ||| || ||   ||  |    |  ||     ||||||| | ||| |||| |||  ||||
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgttt--cctatgc-catgccatgcaaaa---tccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcag

upper sequence: GRMZM2G013079_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 9

ACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaattcatgttcatgacatacagaagtgtctgttcatctaaaggggaactaatgatgccagtgatatttatcag--------------------
  ||||| ||||| || || || || ||||||||||| ||||| || |||||||||||||| || || || ||||| || ||||| ||||| |||||||||||||| || |   | ||| ||  | ||  || || || |      |    || || |    ||    |  | |  |                        
TTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGATCTGGCCACTTACATTTCCATCAACCAgtatgtata-tcatttttcgtgcaacacttaactggctatcttctgatctcggcaccacaactgtgtattttgtacagggattaccagatgagcaattgtt

upper sequence: GRMZM2G013079_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA13G02420.1 (Glycine max), 5'ss of exon 9

ACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaattcatgttcatgacatacagaagtgtctgttcatctaa-----aggggaactaatgatgccagtg-atatttatcag--------------
  ||||||||||| || || || || ||||||||||| ||||| || |||||||||||||| || || || ||||| || || || ||||| |||||||||||||  ||   | | | ||     |||  |  |  || |   |   |     || ||  |||||| || |     | |  | |                 
TTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGATCTGGCCACCTACATTTCCATCAACCAgtatggata-cgcttttccaattagtacttagcttcctatggttgagagtatcagaggggctaatgttgaccccatacaactgtagtgcatgatcaagaat

upper sequence: GRMZM2G013079_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA06G11330.1 (Glycine max), 5'ss of exon 9

ACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgt---ttaattcatgttcatgacatacagaagtgtctgttcatctaaagg--ggaactaatgatgcca-gtgatatttatcag-------------
  ||||| ||||| || || || || ||||||||||| ||||| || |||||||||||||| || || || ||| | || ||||| ||||| |||||| |||| ||   | | ||   || ||  || ||      | |||  | ||||         ||||    ||  |         ||| |||             
TTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGATTTGGCCACTTACATTTCCATCAACAAgtacgtatatcatttttcgtccactacttaactggatatcttctgatctcggtaccataactgtgtatttcgcacagggattaccagattagcaattgtt

upper sequence: GRMZM2G013079_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G77810.2 (Arabidopsis thaliana), 5'ss of exon 9

ACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaattcatgttcatgacatacagaagtgtctgttcatctaaaggggaactaatgatgccagtgatatt-tat-cag
| ||||||||||| ||||| || || |||||||| || ||||| || || ||||| |||||||| || || ||||| |||| ||| || || ||||||||||| ||    |     | | |  |||| |||     |  | |||| || |     |  |  | |      |  || ||| |||
ATTGGAAATTTGGAGAGGATGGTAACAAATACTTTCGACATGCTACAGGACAGATCTATGCCATCTCCAAGGATCTTGCTAATTACATATCCATCAACCAgtacgtact-tctgcatccttttcataaagag----ccttccatcaaatgtttgtcctaaaaggtttacaactttgtatgcag

upper sequence: GRMZM2G013079_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G22015.1 (Arabidopsis thaliana), 5'ss of exon 9

ACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgt---ttaattcatgttcatgacat-------acagaagtgtctgttcatctaaagggga---------actaatgatgccagt-gatatttatcag-----
  ||||||||||| || ||||| || ||||| ||||| ||||| ||||| ||||| |||||||| || || ||||| || || || || || | ||||||||| ||     | || ||| |  |   ||       |  | |   | ||||   | || ||  |         || ||  ||  || | ||| |||  |       
TTTGGAAATTTGGAGAAGAAGGTAACAAATATTTCCGACATGCTACGGGACAGATTTATGCCATATCAAAGGATCTTGCCACATACATATCTAACAACCAgtaagtgaccaactttatggtttttggattttcgacaaggtaagatatgttttaccaagggaaatgagtatcaaccaaacataacatttgatgtttgacttcgcag

upper sequence: GRMZM2G013079_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv07s0031g03090.t01 (Vitis vinifera), 5'ss of exon 9

ACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaattcatg-ttcatgacatacagaagt------gtctgttcatctaaaggggaacta---atgatgccagtgatatttatcag---------
||||||||||||| ||||| || ||||| ||||| || ||||| || |||||||| |||||||| || || ||||| || || ||||| ||  |||||||||| |   |  | ||| ||       ||||||          |    || || |||  |    ||   || ||       || ||| ||           
ACTGGAAATTTGGAGAGGAGGGGAATAAGTACTTTCGGCATGCAACCGGGCAGATTTATGCCATCTCAAAGGATCTGGCCACATATATCTCTGTCAACCAgtaagaacagataatggttttcagtctacagagtctcatagattccatcttccaaaatgtttttatatataatattttaaatttttttctctagtcactg

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|211117513|gb|FL479408.1|FL479408

EST:     CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCA                         GCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT
genomic: CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT

EST: gi|71306960|gb|DR789635.1|DR789635

EST:     CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCA                         GCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT
genomic: CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT

EST: gi|166539787|gb|EG137001.1|EG137001

EST:     TTCAATCAACCA                         GCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT
genomic: TTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT

EST: gi|32792123|gb|CD944359.1|CD944359

EST:     GATCTCGCTACTTATATTTCAATCAACCA                         GCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT
genomic: GATCTCGCTACTTATATTTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT

EST: gi|60358502|gb|DN225475.1|DN225475

EST:     CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCA                         GCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT
genomic: CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT

EST: gi|5525601|gb|AI861494.1|AI861494

EST:     CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCA                         GCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT
genomic: CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT

EST: gi|60396395|gb|DN229264.1|DN229264

EST:     CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCA                         GCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT
genomic: CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT

EST: gi|60395888|gb|DN228758.1|DN228758

EST:     CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCA                         GCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT
genomic: CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT

EST: gi|60398152|gb|DN230968.1|DN230968

EST:     CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCA                         GCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT
genomic: CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT

EST: gi|32940972|gb|CF045791.1|CF045791

EST:     CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCA                         GCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT
genomic: CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT

EST: gi|67018304|gb|CO447053.1|CO447053

EST:     CAGATATATGCCATTNCGAAAGATCTCGCTACTTATATTTCAATCAACCA                         GCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT
genomic: CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT

EST: gi|91869350|gb|EB400347.1|EB400347

EST:     CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCA                         GCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT
genomic: CAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTT

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), 47 (downstream exon)
Score: 84

ACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaa ... tatttatcagGCCTATCTTGCACAAATATGCAAATGAAGACGTGTCGCTTGGATCATGGTTCATTGGTTTGGAAGTTAATCACATTGATGAAAGGAACATGTGCTGTGGA

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 61

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97