ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...atgttttgctttgtttcctctataggttatgaagtttgtggttgtgcaatgccagatctggcatcctcatttcttactgctacatttggccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGGGTCCCCAAGCATCTGAGGGAGG

Basic information

species	Zea mays
transcript	GRMZM2G053801_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g55290.4 (Oryza sativa), 3'ss of exon 3

atgttttgctttgtttcctctataggttatgaagtt-tgtggttgt-gcaatgccagatctggcatcctcatttc-------ttactgctacatttggccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGGGTCCCCAAGCATCTGAGGGAGG----
             |||    |  |  |  ||||| |   |  ||||  |||       || ||||| || || ||       | | |||| | ||| |     || |||||||| || |||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || |||||||||||||||||||||||||| || ||||    
-------------ttttagatgcaaatgctgaagatgcttttttgtcacaagagtttgtcaggcattcttatatcaaatgtatcattgcttctttttgtgtgttttcagccagGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGGAGAA

upper sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g55290.1 (Oryza sativa), 3'ss of exon 4

atgttttgctttgtttcctctataggttatgaagtttgtggttgt-gcaatgccagatctggcatcctcatttc-------ttactgctacatttggccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGGGTCCCCAAGCATCTGAGGGAGG
        |||| |     | |  | | | || | || |  ||||  |||       || ||||| || || ||       | | |||| | ||| |     || |||||||| || |||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || |||||||||||||||||||||||||| || ||||
------cactttttagatgcaaatgctgaagatgctttt--ttgtcacaagagtttgtcaggcattcttatatcaaatgtatcattgcttctttttgtgtgttttcagCCAGGCTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGTGTCTGCCGGGTCCCCAAGCATCTCAGAGAGG

upper sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g63890.1 (Oryza sativa), 3'ss of exon 3

atgttttgctttgtttcctctataggttatgaag-tttgtggttgt-gcaatgccagatctggcatcctcatttc-------ttactgctacatttggccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGGGTCCCCAAGCATCTGAGGGAGG
             |||    |  |  |   |||| |   |  ||||  |||       || ||||| || || ||       | | |||| | ||| |     || ||||| ||||| |||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || || ||||||||||||||||||||||| || ||||
---------cactttttagatgcaaatccagaagatgcttttttgtcacaagagtttgtcaggcattcttatatcaaatgtatcattgcttctttttgtgtgttttcagCCGGGTTATGAGCGCCTTTGCTGTCTTCGATGCATACAGACACGAGACCACAACTTTGCAACTACATGCGTCTGCCGGGTCCCCAAGCATCTCAGAGAGG

upper sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G11450.1 (Glycine max), 3'ss of exon 4

atgttttgctttgtt-----tcctctataggttatgaagtttgtggttgtgcaatgccagatctggcatcctcatttcttactgctacatttggccctc-ttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGGGTCCCCAAGCATCTGAGGGAGG
  ||||| ||||        |  | | |   || || | | | ||  |  |   |    ||| | |  | || |  || |  || |   ||||| |    |||||||| ||||| || || |||||||||||  ||||||| ||| ||||||| ||||| ||||| || |||||||| ||| | || |||||||| || |||||||
--gttttactttcaccaagattttatttcatttgtgcattctatgtgta-gttttcttggattttgagtacttaaatcattatgtt---tttggtctgaattgcagCCTGGTTATGAACGTCTTTGCTGCCTGAGGTGCATGCAGCCACGTGATCACAATTTTGCCACCACTTGTGTTTGCAGAGTACCCAAGCAACTTAGGGAGG

upper sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G28440.2 (Glycine max), 3'ss of exon 5

atgttttgctttgtttcctctataggtt-atgaagtttgtgg---ttgtgcaatgccagatctggcatcctcatttcttactgctacatttggccctc-ttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGGGTCCCCAAGCATCTGAGGGAGG
  || ||| |||  |  | |||    || ||    ||||||     ||||   |    ||| | |  |  | |  || |  || |   ||||| |    |||||||| ||||| || || |||||||||||  ||||||| ||| ||||||| ||||| ||||| || |||||||| ||| | || |||||||| || |||||||
--gtattgttttactgtcactaagattttatttgatttgtgcattctgtgttttcttggattttgagtaattaaatcatcatgtt---tttggtctgaattgcagCCTGGTTATGAACGTCTTTGCTGCCTGAGGTGCATGCAGCCACGTGATCACAATTTTGCCACCACTTGTGTTTGCAGAGTTCCCAAGCAACTTAGGGAGG

upper sequence: GRMZM2G053801_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 3

------atgttttgctttgttt--cctctataggttatgaagtttgtggttgtgcaatgccagatctggcatcctcatttcttactgctacatttggccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGGGTCCCCAAGCATCTGAGGGAGG
      | | |    |||| ||    ||| ||    || ||    |      || | |  ||  ||    |||||   || ||| || ||   ||       |||||||||||||| || || || |||||| |  | ||||| ||  |||| || ||||||||||| || || ||||| ||||||||||||||||| || |||||||
aaaaacaggctgatatttgcttaatttctctaaaagataaaa---gcaaagatgaatttacatctccaaaatcct---tttttaatgatatgctt--ttgaattgcagCCAGGTTATGAACGTCTCTGCTGCTTGAGATGCATGCAACCACGGGATCACAACTTTGCCACCACATGTGTGTGCCGGGTCCCCAAGCACCTAAGGGAGG

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|32913966|gb|CF018778.1|CF018778

EST:     GCCTGGACCAGAGCTATGCAGATCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGATCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|60349645|gb|DN216618.1|DN216618

EST:     GCCTGGACCAGAGCTATGCAGACCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGATACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGATCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|113702562|gb|EE680066.1|EE680066

EST:     GCCTGGACCAGAGCTATGCAGATCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGATCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|37391966|gb|CF633228.1|CF633228

EST:     GCCTGGACCAGAGCTATGCAGATCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGATCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|211435826|gb|FL465189.1|FL465189

EST:     GCCTGGACCAGAGCTATGCAGATCGTAACCTGATCGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTG-CTTCGGTGCATACAGACACGTGACCAC
genomic: GCCTGGACCAGAGCTATGCAGATCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCAC

EST: gi|166658294|gb|EG267248.1|EG267248

EST:     GCCTGGACCAGAGCTATGCAGATCGTAACCTGATTGCAAAGTGGAAAAAG                         CCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGC
genomic: GCCTGGACCAGAGCTATGCAGATCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGC

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: 305

TGATCTTTACTACAGAAGGAAGGAGATATCACGGGAGCTTTATGAGTTCTGCCTGGACCAGAGCTATGCAGATCGTAACCTGATCGCAAAGTGGAAAAAGgtaattatcc ... cctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGGGTCCCCAAGCATCTGAGGGAGG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 218

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 275

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 198

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gcaatgccagatctggcatcctcatttcttactgctacatttggccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGGGTCCCCAAGCATCTGAGGGAGG

                         ttcttac  putative branch site (score: 198)
                                            ccctcttgc  putative PPT
                       atttctta  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttttgctttgtttcctctataggttatgaagtttgtggttgtgcaatgccagatctggcatcctcatttcttactgctacatttggccctcttgcagCCAGGTTACGAGCGCCTTTGCTGCCTTCGGTGCATACAGACACGTGACCACAACTTTGCAACGACTTGTGTCTGCCGGGTCCCCAAGCATCTGAGGGAGG

- -ttttgct
- - - - - - - - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - - - - - -gcaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctacat