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

gtaacaataacatatagttgttcctcggaaaaaaggggcaccaaatagttggtttatatatgcggacatattatttatgataattctcgtctgttttcatgcagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG

Basic information

species	Zea mays
transcript	GRMZM2G124883_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 17

gtaacaataacatatagttgttcctcggaaaaaaggggcaccaaatagttggtttatatatgcggacatattatttatgataattctcgtctgttttcatgcagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG
                           | || |    |      |||| || | ||  |     | | || || ||    |||  ||  |  | |||| || |||||| |||||||||||||| |||||||||||||| || || |||| || ||||||||||||||| ||||| ||||| || ||||||||||||||||||||
---------------------------gtaacatatagttgttgatagatg-tgtacgtggataggcttactagtttgcctaa--cttatgcgctttcttgtagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAACCCTGATATTGAATCATATTCAGAAACCATAAGTACTTTAAAATTTGCTGAAAGGGTTTCTGG

upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G35130.1 (Glycine max), 3'ss of exon 15

gtaacaataacatatagttgttcctcggaaaaaaggggcaccaaatagttggtttatatatgcggacatattatttatgataattctcgtctgttttcatgca--gGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG
       |||    |  ||  || |  |  |         ||    |  |  | ||| ||      | ||| || | |||   || || |   ||||  ||||  ||||  ||||| |||||||| |||||||||||||||||| | ||     | |||||||| |||||| | |||||||| |||||||||||||||||||||||
------gtaaatctttattcatcatttgttatgtcacatgccttgaatcttttctatgtagattttcttatgatctttgactcttgtctttgattttattgcacagGTGACCAAGCGAAGACACTCATGTTTGTTCAAATTAATTCAGACGTAAGTTCATATTCTGAAACACTGAGCACTTTAAAGTTTGCTGAAAGGGTTTCTGG

upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17

-------------------gtaacaat--aacatatagttgttcctcggaaaaaaggggcaccaaatagttggtttatatatgcggacata--ttattta-tgataat--tctcgtctgtttt-catg-cagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG
                   ||| ||||  |   ||| ||| |   | |    |   |    |    |  ||     |||| ||| | |||   ||| | | |   |||    | ||| ||| |  |||  |||||| ||||| || || || |||||||| ||  ||||||| |||  ||  |||||||| |||||  ||||||| ||||||||||||||| ||||||||||
gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgcattttgatttaagcatat-tgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG

upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 3'ss of exon 16

gtaacaataacatatagttgttcctcggaaaaaaggggcaccaaatagttggtttatata--tgcggacatattatttatgataattctcgtctgttttcatg---cagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG
                               ||      | |   |  |  |||| |  |   | |  |  | | ||     | ||    || || ||| |     ||||||| | |||||||||||| |||||||||||| | ||||| |||| |   |||||||||||  |||| || |||||||| || || ||  | || |||||
----------------------------gttaactccaaatcttctgctctgttttttcaatcgtgatcgaaattttctaacttatctctgtgtgatttaacatcacagGTGGTCGAGCAAAGACACTAATGTTTGTTCAACTGAATCCTGATATTACTTCATATTCAGAGTCAATGAGTACTTTGAAATTCGCAGAGCGTGTCTCTGG

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|32834464|gb|CD974142.1|CD974142

EST:     TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAG                         GTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGAT
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacaataa ... tttcatgcagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGAT

EST: gi|213168610|gb|FM190648.1|FM190648

EST:     TGTTCCTTATCGAAACAGCAAGCTGACTNNNGTTCTACAGAGCTCTTTAG                         NNGGGCAAGCAAAGACACTGATGTTTGTTCAAATTA-TCNNNATACTGGAT
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacaataa ... tttcatgcagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGAT

EST: gi|76281863|gb|DV021431.1|DV021431

EST:     TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAG                         GTGGGCAAGCAAAGACACCTGATGTTTGTTCAAATTAATCCGGATACTGGA
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacaataa ... tttcatgcagGTGGGCAAGCAAAGACAC-TGATGTTTGTTCAAATTAATCCGGATACTGGA

EST: gi|211077350|gb|FK960594.1|FK960594

EST:     TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAG                         GTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGAT
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacaataa ... tttcatgcagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGAT

EST: gi|211077349|gb|FK960593.1|FK960593

EST:     TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAG                         GTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGAT
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacaataa ... tttcatgcagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGAT

EST: gi|211077348|gb|FK960592.1|FK960592

EST:     TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAG                         GTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGAT
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacaataa ... tttcatgcagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGAT

EST: gi|76018056|gb|DT945226.1|DT945226

EST:     TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAG                         GTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGAT
genomic: TGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacaataa ... tttcatgcagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGAT

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: 482

CTCTCTGCTCTTGGTGATGTGATTTTTTCTTTGGCACAGAAAAATGCCCATGTTCCTTATCGAAACAGCAAGCTGACTCAAGTTCTACAGAGCTCTTTAGgtaacaataa ... tttcatgcagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 81

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 58

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 331

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tggtttatatatgcggacatattatttatgataattctcgtctgttttcatgcagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG

                                  ttctcgtctgttttc  CT-rich tract
                acatattatttatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaataacatatagttgttcctcggaaaaaaggggcaccaaatagttggtttatatatgcggacatattatttatgataattctcgtctgttttcatgcagGTGGGCAAGCAAAGACACTGATGTTTGTTCAAATTAATCCGGATACTGGATCATATTCAGAAACAATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG