ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgctgcgtttatctctggctccttgtttttatgcactaatccaatgaggctgaactcttgttgtcaattgcaaaag

Basic information

species	Zea mays
transcript	GRMZM2G063949_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 6

TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttg-ctgcgtttatctctggctcctt-gtttttatgc---actaatccaatgaggctgaact----cttgttgtcaattgcaaaag
||| || ||  | |||||| |||| ||||||||||| || ||||| |||||||| ||||| ||||| |||||||| || ||||||||     |||||||||||||||  ||  |||||||| |   ||||| | | ||||||   | | | |   | ||  ||||||      |||  |  ||  ||||||
TCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGATTgtatgttttctctgtttatctttacttcctttgctcttatgctagatttaccttgttag-ttgaactgaaatgtgtactttatgtcaaaag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA17G05440.1 (Glycine max), 5'ss of exon 4

TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgctgcgtttatctctggctccttgtttttatgcactaatccaat----gaggctgaactcttg-ttgtcaattgcaaaag------------------------------------
||| |||||  |||||||| | |||||||| ||||| ||||| || ||||| || ||||| || || ||||||||||| ||||| ||  |  ||||||||||| ||| |    |  | || |   |      ||||| | ||| |||  ||    || | | | || |||  | | | |                                            
TCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGATTgtaggttcccatatgaaactttatata-----ttttaagtactgatctgattgtagaagttcatcttttgactattattcttgtttcatggttcaactaaatgtgaacgataatttttaacag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 6

TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgctgcgtttatctctggctccttgtttttatgcact---aatccaatg-aggc---tgaactcttgttgtcaattgcaaaag---------------------------------------
||| ||| |  |||||||| | |||||||| || || || ||||| |||||||||||||| ||||| || |||||||| ||||||||  |||||||||||||| |||     || ||||| |   |    |  | | ||   |   ||| | ||  |||    ||   | || || |||| |  ||                                          
TCTTCTCAGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTTGTTTACATTAAAGATGCTATTGAAGCTGTCTTGCTGATGATTgtacgttctaatgtctatctttatttttgggactgtttgttttttaaataccatacaggtccatgtgatttttttttcaagtcaaattattgttggctggtccactgagtgttatgacctgttaacag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 6

TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttg-------ctgcgtttatctctgg--ctccttgt-ttttatgcactaatccaatgaggctgaactcttgttgtcaattgcaaaag---------------------------------------
||| |||||  |||||||| | |||||||| || || || ||||| |||||||||||  | ||||| || |||||||| ||||||||  || ||||||||||| |||        ||   ||||| | |||  ||  |||| |||||   ||  || || || |  |    | |  |  ||||||      |                                       
TCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaatacagattca-tgtga-tattttttcatgttcaattattgttgttgtcagctggtccactgagtgttatgacctgttaacag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA11G19550.2 (Glycine max), 5'ss of exon 6

TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttg-------ctgcgtttatctctgg--ctccttgt-ttttatgcactaatccaatgaggctgaactcttgttgtcaattgcaaaag----------
||| |||||  |||||||| | |||||||| || || || ||||| |||||||||||  | ||||| || |||||||| ||||||||  || ||||||||||| |||        ||   ||||| | |||  ||  |||| |||||   ||  || || || |  |    | |  |  ||||||      |          
TCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaatacagattca-tgtga-tattttttcatgttcaattattgttgttgtcagctg

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 6

TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgctgc----gtttatctctggc-------tccttgtttttatgc-actaatccaat-gaggctgaact-cttgttgtcaattgcaaaag
||| || ||  | |||||  | |||||||| ||||| ||  | || |||||||||||  |||||||||| |||||||||||||||||  |  ||||||| ||  ||| |       | ||||| ||||           ||||||||||   | |||   | | |   ||||| | ||||  |     |  |  ||
TCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagtttcattcattgcttatccctggtgatatatcgtttgtttttatattattaaagaagttgcatctgaattgcttgcggaattctttaccag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6

TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgctgcgttt-atctctggctccttgtttttatgc-actaatccaatgaggctgaactcttgttgtcaattgcaaaag-------------------------
||| || ||  | |||||  | |||||||| ||||| ||  | || |||||||| || ||||||||||| |||||||| ||||||||  |  ||||||||||| ||| |   |  | || | | |||  ||||||  |  |   ||||   |  ||   ||| |  | |   | |   |  |                           
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgttaatgttagaagttcgaagtagtttcaactaaaacctataatgacattgtatgtttgtggttcag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 6

TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgctgcgtttatctctggctccttgtttttatgc---actaatccaatgaggctgaactcttgttgtcaattgcaaaag-----------
 || || ||  | |||||  | |||||||| ||||| || || || |||||||||||||| || || ||||||||||| ||||| ||  || ||||||||||  ||||       | ||| |   |   || ||  |        | |       |     ||  |  | ||   | |   |              
CCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgtgagttgaccatcctttctttcattatatgattccacatttagtttacttggaaaaaaaaaaaacaggatgctgaatattatgatcttttctcag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6

TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgctgcgtttatctctggctccttgtttttatgcactaatccaatgaggctgaactcttgttgtcaattgcaaaag-----------
 || || ||    |||||  | |||||||| ||||| || || || |||||||||||||| ||||| ||||||||||| ||||| ||  || ||||||||||  || |       |  || |   |   || ||  |     ||    | |  |    ||     ||||   | | | |              
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggaccatccttcctttcattatctgattccacat-ttagcttacttggaaaaaaaaaaggttgctgaatactatgatattttctcag

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|22715502|gb|BU197799.1|BU197799

EST:     GAACCTTTGTCTACATCAAGGATGCCATCGAAGCTGTAGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAACGGCCACATCTTCAA
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAATGGCCACATCTTCAA

EST: gi|93281900|gb|EB674164.1|EB674164

EST:     GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC

EST: gi|109637685|gb|EC591230.1|EC591230

EST:     GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATT                         GAAAAATCCTGCTCGAGCCAATGGGCCACATCTTCAATGGTGGGGAATCCG
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAA-TCCTGCTCGAGCCAATGG-CCACATCTTCAATGTTGGG-AATCCG

EST: gi|149086197|gb|EE175737.2|EE175737

EST:     GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAA
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAA

EST: gi|40337281|gb|CK371351.1|CK371351

EST:     GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC

EST: gi|60356652|gb|DN223625.1|DN223625

EST:     GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC

EST: gi|32868566|gb|CF008248.1|CF008248

EST:     GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC

EST: gi|67020590|gb|CO449339.1|CO449339

EST:     AACCCTTGCCTACATCA-GGATGCTATCCGA-GCTGTAGTGCTGATGATT                         GAAAATCCTGCTCGAGCCA
genomic: AACCTTTGTCTACATCAAGGATGCTATC-GAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCA

EST: gi|149086196|gb|EE175736.2|EE175736

EST:     GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC

EST: gi|31356398|gb|CD440755.1|CD440755

EST:     GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATT                         GAAAATC-TGCTCGAGCCA
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCA

EST: gi|7137694|gb|AW499223.1|AW499223

EST:     GAACCTTTGTCTACATCAAGGATGCCATCGAAGCTGTAGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAACGGCCACATCTTCAATGTTGGGAATCCGAAC
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC

EST: gi|211216490|gb|FL245940.1|FL245940

EST:     GAACCTTTGTCTACATCAAGGATGCCATCGAAGCTGTAGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC

EST: gi|60353566|gb|DN220539.1|DN220539

EST:     TATCGAAAGCTGTAGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC
genomic: TATCG-AAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC

EST: gi|31355714|gb|CD440071.1|CD440071

EST:     GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATT                         GAAA-TCCTGCTCGAGCCAATGGCCACA
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAATGGCCACA

EST: gi|211213926|gb|FL245933.1|FL245933

EST:     GAACCTTTGTCTACATCAAGGATGCCATCGAAGCTGTAGTGCTGATGATT                         GAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC
genomic: GAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAAC

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: 237

TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgct ... attgcaaaagGAAAATCCTGCTCGAGCCAATGGCCACATCTTCAATGTTGGGAATCCGAACAATGAAGTTACCGTTAGGGAGTTGGCCCAAATGATGACAGAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 38

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 125

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgctgcgtttatctctggctccttgtttttatgcactaatccaatgaggctgaactcttgttgtcaattgcaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT