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

...ttttagtgtgtgtattacccaatttgctttaactatgtctgagcatatagtactttatggttccatttgacattgctgatgttttgttttggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT

Basic information

species	Zea mays
transcript	GRMZM2G056569_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 4

-ttttagtgtgtgtattacccaatttgctttaactatgtctgagcatatagtactttatggttccatttgacattgctgatgttttgttttggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT-
 || || ||||     |     |||   | |        |       || || ||   |    |  | | ||  || || || | | || ||  | | |||||||| ||||| || |||||||| ||||||||||||||||||| |||||||||||||||||| ||||| ||||| |||||||  |   | || |  | |  
tttataatgtgctcgctcattgattatgtctggaagaaacaatttgcatggtcctcacttccacattcttaccgtggtg-tgctgttttatgatttcacagGTGACACATGCTGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAGGAAGGTGTGCCGGAGGGTCTTTACATGTGATGTGC-TCACTGGTCGC

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5

ttttagtgtgtgtattacccaatttgctttaactatgtctgagcatata-----gtactttatggtt--ccatttgacattg---ctgatgt-tttgttttggat--acccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT
       | |  | ||| ||| |||  || ||  |  |   | || | |       ||    |||      | | | || ||   || |||| |||   ||||||     |||||||| ||| | |||||||||||||||||||||||||| |||| ||||||||| ||||| || || || || |||||||||||  |      || |  | 
----gtagagactcttaacca-tttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAATTATAATCATATCG

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5

ttttagtgtgtgtattacccaatttgctttaactatgtctgagcatatagtactttatggttccatttgacattgctgatgttttgttttggat--acccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT
       ||  | |||  |    ||      ||| ||  | | |  |  | | | | ||  |   |||    |  |   ||||| || ||  ||      ||||||| ||||  || |||||||| || ||||||||||| |||| ||||||||| ||||| ||||| || ||||| |||||||    || |      | ||
-------gtaaggattctctggcttctcaccact-tgattcatcgaac-gcaatctttgaataattttactttaacctttgtttggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5

---ttttagtgtgtgtattacccaatt-tgctttaactatgtctgagcatatagtactttatggttccatttgacattgctgatgttttgttttggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT--
         ||  || ||||||  | |     ||  ||   | |   ||  ||| ||   | | | ||| || |  |||    || ||   |   |     |||||||| |||| ||| |||||||| ||||||||||||||||||| ||||||||| ||||| || || || || || |||||||   | ||  || || | |  
ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggacc--aggatcccaattaaatttg--actggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGA-AAACA-CTGCTACATAT

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 4

-------------------------------ttttagtgtgtgt--attacccaatttgctttaactatgtctgagcat-atagtactttatggttccatttgaca--ttgctgatgttttgttt--tggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT
                                 | | ||   |   |||  |||  |    | ||  |    ||    | ||   |     ||||| | | | |    ||| |  |||||||  |  ||      |||||||| || |  ||||||||||| || || |||||||| ||||| ||||||||||||||||| || || ||  | |||||||||   |           |
gtaagattgtcgtcttttgtactttgcagttcgtgaatggaggctaattgaccagctgaaatgaataaaagttgcttttgatcaaaagacctggtttcttgtaatgagttgttattgttttggatggtgatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAGAAGGAAGGTGTACCTGAGGGATTATACATGTAGATTATTCAGTGCAGGT

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 5

-----------------------------------------------------------ttttagtgtgtgtattacccaatttgcttta--actat-gtctgagcatatagtactttatggttccatttgacattgctgatgttttgttttggatacc-cagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT
                                                           ||  | | | |   || |||   | ||| ||  | |   | ||  | || | |    || || |||  |     | |  |||   |   || |  || || |||||||| || || || |||||||| || ||||| || |||||||||||||||||||||||||| || || ||  | || |||||| | ||     |     
gtgagcttgccatttctttgtattcttttatatgtatttttaatgcgtctcgtcagaggttacacttttttagttgccctcatggctgtataattgcaggctttgaat-tggcttgttttgattctgtgactaagtattgactgtggattcttaatgccacagGTGACTCAAGCGGACTTCAAGAAGGCTAAGGACAAAGTGATGTACAAGAAGAAGGAAGGTGTACCCGAGGGGTTATATATGTAGAATACTCAGTCAAGTG

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 5

ttttagtgtgtgtattacccaatttgctttaactatgtctgagcatatagtactttatggttccatttgacattgctgatgttttgttttggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAG-TAGACGTCTCCTGCCT
                                               ||||   |    | |       || ||  ||      | || |   |  |||||| || || || ||||||||||| || || |||||||| |||||||||||||| ||||| || ||||| || || ||||||||  ||| |||| || || |
----------------------------------------------gtagtttctcgatgcttttcacaactttcttgtaacgattttcttcttctccagGTAACTCAAGCTGATTTCAAGAAGGCGAAAGAGAAGGTCATGTACAAGAAGAAAGAAGGCGTCCCGGAGGGCCTGTACATGTAAATAGCCGTC-CCAGCTT

upper sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 5

ttttagtgtgtgtattacccaatttgctttaactatgtctgagcatatagtactttatggttccatttgacattgctgatgttttgttttggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT
                                               ||||   | |  | |       || ||  ||      | || |   |  |||||| || || || ||||||||||| || || |||||||| |||||||||||||| ||||| || ||||| || || ||||||||     |    || || |
----------------------------------------------gtagtttctcaatgcttttcacaactttcttgtaacgattttcttcttctccagGTAACTCAAGCTGATTTCAAGAAGGCGAAAGAGAAGGTCATGTACAAGAAGAAAGAAGGCGTCCCGGAGGGCCTGTACATGTAAATAGCCATCCCAGCTT

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|113702544|gb|EE680048.1|EE680048

EST:     CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAA                         GTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG
genomic: CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAAgtgagcctga ... ggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG

EST: gi|166680104|gb|EG225400.1|EG225400

EST:     CGTAGAATGAAA                         GTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG
genomic: CGTAGAATGAAAgtgagcctga ... ggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG

EST: gi|45568169|gb|CK985936.1|CK985936

EST:     CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAA                         GTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG
genomic: CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAAgtgagcctga ... ggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG

EST: gi|9953765|gb|BE640348.1|BE640348

EST:     GTAGAATGAAA                         GTGACCCATGCAGATTTCAAGAAAAC-AAGGAGAAGGTGATGTACAAGAAG
genomic: GTAGAATGAAAgtgagcctga ... ggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG

EST: gi|62550417|gb|DN830837.1|DN830837

EST:     CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAG                         GTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG
genomic: CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAAgtgagcctga ... ggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG

EST: gi|116828199|gb|EC855484.1|EC855484

EST:     CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAA                         GTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG
genomic: CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAAgtgagcctga ... ggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG

EST: gi|166430147|gb|EG115061.1|EG115061

EST:     CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAA                         GTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGG
genomic: CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAAgtgagcctga ... ggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGG

EST: gi|14203652|gb|BG837329.1|BG837329

EST:     CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAA                         GTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG
genomic: CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAAgtgagcctga ... ggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG

EST: gi|32937106|gb|CF041925.1|CF041925

EST:     CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAA                         GTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG
genomic: CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAAgtgagcctga ... ggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG

EST: gi|211285728|gb|FL480875.1|FL480875

EST:     CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAA                         GTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG
genomic: CCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAAgtgagcctga ... ggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 495

GGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCACGGAGGCTGGATTGCTCGCCTTAAGAGAACGTAGAATGAAAgtgagcctga ... ggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 318

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 266

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tatagtactttatggttccatttgacattgctgatgttttgttttggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT

                            tgctgat  putative branch site (score: 266)
                                    ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttagtgtgtgtattacccaatttgctttaactatgtctgagcatatagtactttatggttccatttgacattgctgatgttttgttttggatacccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - tttgctt
- - - - - - - - - - - - - - - - - atgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgatg