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

gtaacctcctacacttattcctccccgccgactctcgttgtgcagatgtttttgtatcgtgttctgattccgtgacgactgttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG

Basic information

species	Zea mays
transcript	GRMZM2G178341_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 1

gtaacctcctacacttattcctccccgcc--gactctcgttgtgcagatg--tttttgtatcgtgttct------gattcc--gtgacga--ctgttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG
||||||| || | ||   | |||| | ||   | || |||     |   |  || | ||  ||  | ||      || ||    || ||   ||||  |||||||||||||||||||| ||||||||||| || || ||||||||||||||||||||||| ||||||||||||||||||||||||||  | |||||||| ||||
gtaaccttct-cgctcgcttctcctctcctccattcccgtctccgattcgccttctcgtgacgcctcctctgactgactctcgttggcgcttctgtccccgcagTCGCTGATCGCCGGGGAGGACTTCCAGCACATCCTGCGTCTGCTGAACACCAACGTCGATGGGAAGCAGAAGATCATGTTCGCGCTCACCTCCATCAAGG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 1

------gtaacctcctacacttattcctccccgccgactctcg---ttgtgcagatgtttttgtatcgtgtt-ctgattccgtgacgactgttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG
         |  |   | ||| | || |          | |     |||||||  |||  || |    ||   ||||||       | ||  |     |||||||| | ||   |||||| ||||| || || || ||| |  ||||||| ||||| ||||||||||||||||| ||||||||  | ||||| || || |
gaaatcaagatttttgaaactgactcttgttttggatatgtaaaaattgtgcatttgtaattttggtttgaaactgattgatccttgtcttgttttatagTCGCTGGTGGCAAACGAGGATTTCCAGCACATACTTCGTGTTTTGAACACGAACGTAGATGGGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G36880.3 (Glycine max), 3'ss of exon 1

-----------gtaacctcctacacttattcctccccgccgactctcgt----tgtgcagatgtttttgtatcgtgttctgattccgtgacgactgt-------------tgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG
            ||   |  | ||| | | ||| | |  ||    | |     |     |||  | || |   |    || | ||  | ||   | |             ||  |||||| ||| | ||   |||||| ||||| || ||||||||| |||||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||
gtgcgctcccattattttattgcacctctcccttcacaacgttgattgaacaataaaaggattctattttgaggaacccttaatcgataactgatttctttttttgtgtgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G36610.3 (Glycine max), 3'ss of exon 1

--------gtaacctcct-acacttattcctccccgccgactctcgttgtgcaga------tgtttttgt----------atcgtgttctgattccgtgacgac-tgt-tgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG
         | |  || |  ||| | | ||| | |  ||    | |    | | |         |||||           ||||   |||||||   |       ||| ||  |||||| ||| | ||   |||||| ||||| || ||||||||| |||||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||
gcgctctcattatttcatcgcacctctcccttcacaacgttgattgaaaagaaaaaagattcaattttgaggaacccttaatcgatatctgattttttttttttgtgtgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G08690.1 (Glycine max), 3'ss of exon 1

----------------------------------------gtaacctcctacacttattcctccccgccgac--tctcgttgtgcagatgtttttgtatcgtgttctga----ttccgt----gacgactgttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG
                                        |   | ||  |   ||  |  |  |    | |  | ||     ||   | |||| |    || ||  ||    |  | |     | |  | |     ||||| ||| | ||   |||||| ||||| || ||||||||| |||||||||||||||| ||||||||||||||||| ||||||||  | ||||| || || |
gtacgatttcagcgtttccgaattgattttgataaacaaagattcttcaaaagattcgttttatcttttggcaatttcaaaaggcgatttttttggctctgtttttggaggagtcacattttaaatggttttgcttacagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTAGATGGGAAGCAGAAGATAATGTTCGCTCTCACCTCTATCAAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G36610.2 (Glycine max), 3'ss of exon 1

----------gtaacctcct-acacttattcctccccgccgactctcgttgtgcaga------tgtttttgt----------atcgtgttctgattccgtgacgac-tgt-tgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG
           | |  || |  ||| | | ||| | |  ||    | |    | | |         |||||           ||||   |||||||   |       ||| ||  |||||| ||| | ||   |||||| ||||| || ||||||||| |||||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||
gtgcgctctcattatttcatcgcacctctcccttcacaacgttgattgaaaagaaaaaagattcaattttgaggaacccttaatcgatatctgattttttttttttgtgtgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G30970.1 (Glycine max), 3'ss of exon 1

--------------------------------------gtaacctcctacacttattcctccccgccgactctcgttgtgcagatgtttttgtatcgtgttctgattccgtgacgactgttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG
                                       |||      | |     |           || ||   |  | |  ||  ||||| |  | ||    |   |||  |  |  ||  |||||| ||| | ||   |||||| ||||| || ||||||||| |||||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||
gtacgttcccatttcatcgaacctctccgagcgcgacgttaattgaaaaaaaaggattactttgaggaacccttaatcggtaactgaatttgttt--tttttgtgtgttgtgctgtgttgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCTATGACCTCCATCAAGG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv18s0072g00060.t01 (Vitis vinifera), 3'ss of exon 2

gtaacctcctacacttattcctccccgccgactctcgttgtgcagatgtttttgtat-cgtgttctgattccgtgacgactgttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG-------------------
|||| |       |    || || |   |  |  |     |||  ||  |||  | | ||| |  | | ||  |  ||   |  |   ||||||||  | ||   ||| || ||||| || ||  ||||| | |||||||| |||||||||||||| |||||||| ||||| ||| | || || || ||||                   
gtaatcagggtttcaatctcttctcgttcttcctttagaatgcctataatttaatgtacgtttgttcaatcttt--cgttgg--gttacagtcgctagtggcgaacgaagAATTCCAGCACATATTGCGTGTCCTGAACACGAACGTGGATGGGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGC

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 1

gtaacct--cctacacttattcctccccg-ccgactctcgttgtgcagatgtttttgtatcgtgttctgattccgtgacgactgttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG
|| |     | |    | ||| ||       | | ||| ||   | | ||| || | | |  |||| || |   |    |  | ||   |||||| ||  | ||   |||||| || || || ||||| ||| |||| ||||||||||| ||||||||||||||||||||||| ||| | || ||||| ||||
gtgagtgggcttgttttcatttctgttaaatcaattcttgtgtcgaatatggttgtttgt--tgttatgttaatgaattggatttt---gcagTCTCTTGTTGCAAACGAGGAATTTCAGCACATTCTTCGTGTGCTCAACACCAACGTCGATGGGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S14_438V6.1 (Physcomitrella patens), 3'ss of exon 1

-------------------------------------------------gtaacctcctacacttattcctccccgccgactctcgttgtgcagatgtttttgtatcgtgttctgattccgtgacgactgttgccgc-agTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG
                                                 ||  | | ||      | |  |    ||      |    |||   | |||  || ||| |    || ||| |  | |   | ||   | ||||||| ||||| || || || || ||||||||||| ||| ||||||| || ||||| |||||   ||||||||||||||||||| |||||||||| || |
gtgggtagtttctcccacctgtgctacacgtaaaaatttcagtttttcggttccgttctgtttggagtgttttttgctcgactttagggtgtgcaggttcatg-atc-taaattggttcag-aatggtgggtgtgactagTCGCTCATCGCGGGTGAAGAGTTTCAACATATTCTTCGTGTGCTGAATACAAACGTCGATGGACGGCAGAAGATCATGTTCGCCCTGACCTCCATTAAAG

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S72_222V6.2 (Physcomitrella patens), 3'ss of exon 1

-----------------------------------------------------------gtaacctcctacacttattcctccccgccg-actctcgttgtgcagatgtttttg-tatcgtgttctgat--tccgtgac---gactg--------ttgccg-------cagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG
                                                            |    || | |  |   || |   ||      | | |||||||| ||||||  | | |   | | |||   |  |||||   |  ||        |||  |       ||||||||  | || || ||||| |||||||||||||| ||| |||| ||||| ||||| |||||    |||||||||||||| ||| ||||||||       
gtgtgtagtttcccctccctctgctgtgtgcacaagctggatttttttcttttcattttctcggttctttctttctgtcattttcgttatggtttggttgtgcacatgtttgagattttagggtttgaaggtatgtgaccctggttggtttggttttgttgaagCGGCCAGTCGCTCGTTGCGGGTGAGGAGTTCCAACATATTCTTCGTGTGCTCAACACGAACGTCGATGGACGTCAGAAGATCATGTTTGCCCTGACCTCC-------

upper sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S72_222V6.1 (Physcomitrella patens), 3'ss of exon 1

-----------------------------------------------------------gtaacctcctacacttattcctccccgccg-actctcgttgtgcagatgtttttg-tatcgtgttctgat--tccgtgac---gactg--------ttgccg-------cagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG
                                                            |    || | |  |   || |   ||      | | |||||||| ||||||  | | |   | | |||   |  |||||   |  ||        |||  |       ||||||||  | || || ||||| |||||||||||||| ||| |||| ||||| ||||| |||||    |||||||||||||| ||| |||||||||| ||||
gtgtgtagtttcccctccctctgctgtgtgcacaagctggatttttttcttttcattttctcggttctttctttctgtcattttcgttatggtttggttgtgcacatgtttgagattttagggtttgaaggtatgtgaccctggttggtttggttttgttgaagcggccagTCGCTCGTTGCGGGTGAGGAGTTCCAACATATTCTTCGTGTGCTCAACACGAACGTCGATGGACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGG

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|15312798|gb|BI478389.1|BI478389

EST:     GATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: GATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC

EST: gi|211506692|gb|FL164921.1|FL164921

EST:     GCTGTCGCCGCCTCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: GCTGTCGCCG-C-CTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC

EST: gi|211504327|gb|FL164902.1|FL164902

EST:     GCTGTCGCCGCCTCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: GCTGTCGCCG-C-CTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC

EST: gi|211004160|gb|FL323112.1|FL323112

EST:     GCTGTCGCCGCCTCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: GCTGTCGCCG-C-CTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC

EST: gi|211506690|gb|FL164919.1|FL164919

EST:     TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC

EST: gi|211075481|gb|FL340028.1|FL340028

EST:     TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC

EST: gi|211506702|gb|FL164931.1|FL164931

EST:     TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC

EST: gi|211415860|gb|FL164865.1|FL164865

EST:     TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: TTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC

EST: gi|211504335|gb|FL164910.1|FL164910

EST:     GCTGTCGCCGCCTCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: GCTGTCGCCG-C-CTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC

EST: gi|211504333|gb|FL164908.1|FL164908

EST:     GCTGTCGCCGCCTCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATG                         TCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC
genomic: GCTGTCGCCG-C-CTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACC

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: 371

CGCCGTCTCCTAAACCTTAGCCGCGCGGACGCCCACCAGCAGCTGCCCCCTTGCTGTCGCCGCCTCTCCGCGCGACCGATCTACCGCCGCCGCCACCATGgtaacctcct ... gttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 226

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cgttgtgcagatgtttttgtatcgtgttctgattccgtgacgactgttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG

                          ttctgat  putative branch site (score: 204)
             tttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacctcctacacttattcctccccgccgactctcgttgtgcagatgtttttgtatcgtgttctgattccgtgacgactgttgccgcagTCGCTGATCGCCGGCGAGGACTTCCAACATATTCTGCGTCTGCTGAACACCAACGTGGATGGGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA