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

gtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC

Basic information

species	Zea mays
transcript	GRMZM5G804893_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g38820.5 (Oryza sativa), 3'ss of exon 1

----------------gtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggag--tggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC
                ||     || |   || |     ||||  || |    || ||| ||  || ||| |||  | | | ||   | |||  |||| |   ||    |    ||  || |   ||    ||| |  ||      | || ||| ||||| || || ||||||||||||||||| ||||||||||| ||||||||  |||||||||| |||||||||||||| || || |||||||| || |||
gtgagtcgtcgccctcgtcctcccccctcttgtgctctgctct-gctctgctctgtcttcttttgagttttgagctttgagctcgttg-tttgacttgtcgttggcggcgatgagatgtgactgggtttttgttgtggtggggcaacattacagGGCGAGCGATAAATGCCAGAGGGAGAAGCGCAAGACCATCAACGGCGACGACTTGCTGTGGGCGATGGCCACGCTGGGCTTCGAGGACTACATCGAGCCC

upper sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G33550.2 (Glycine max), 3'ss of exon 2

---------------------------------------------------gtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC
                                                    |  ||   | ||||     ||  | ||| | |      ||   ||   |||||  | |    ||  ||| ||  |  |     |  |||| |  | |||          |||||  || |         |||||| |||||||| || ||||||| ||||||| | ||||| |||||||| |||||| | || ||||||||||| ||  | |||||||||||||||||||| || 
gtgagtcagttattagcaactatacatatccagttatcgatatcaaatgttttttgttttttagctcaaaatgttttttaatgtaaagctgcagttttttaatttttatt---ttttggggattgggggttctgagaattttttaattactgaattccacgcacgtggttat---tatgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCG

upper sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G34050.1 (Glycine max), 3'ss of exon 1

--------------------------------------gtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttc---agggctttagcttggctggggttttgtgt-tgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC
                                      ||   |   | ||||     || || ||  ||||   ||| |  |||    |||  | |    ||     ||| || ||  |  ||| |  ||||| | |  ||         |||||| ||| | || ||    ||||| |||||||| || ||||||| ||||||| | ||||| |||||||| |||||| |||| ||||||||||||||  | || |||||||||||||| || || 
gtcagttagcaactatacatatccatatcaaatgttttgtttttattt-agctcaaaatgtctttttttttttaatggatgattgcagttttttatttttattttttggggattgagggtttctgagaatttgtttatttctgaattccacccacgtgtttatttcggcg---tgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTGCTATGGGCCATGGCCACTTTAGGATTTGAAGACTACATAGAGCCG

upper sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G53340.1 (Arabidopsis thaliana), 3'ss of exon 2

gtaagtgcctcagctgcggct----gactcttacttttgc-ttggcttgttgggaatttggagtggcgttcagggcttt----agcttggctggggttttgt--gttgacttgt------------ccatgtccacgttt---ttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC
|||| | | |   || |         | | |||| |||   |||  ||| |||  ||   | ||   |  |    ||||    || | |  ||  ||| | |   |||  ||||            | ||||| |  ||    | ||||     ||||  || || ||||| |||||||| || |||||  |||||||||||||||| || ||| |||| ||||| ||||||||  | || || ||||| ||||| || |||
gtaatttctttctctactttctcaaaaatgttacctttttgttgctttggtggttatagcgtgtaaagccctcttctttgttaagttagattgatgttatattcattgggttgttaagcaaagtcactatgtcgattttggaatattgttttgccttt-tagGGCTAGTGATAAGTGCCAAAGAGAGAAAAGGAAGACCATCAATGGAGATGATTTGCTTTGGGCTATGGCCACTTTAGGATTCGAAGATTACATCGATCCC

upper sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g03490.t01 (Vitis vinifera), 3'ss of exon 1

gtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC
                             |||||| ||    |   || ||     |  || |||  ||  |||   ||        |||||| || | || || |  |  |     | |  || |   |||| |||||||||||||||||||||| ||||||| ||||||| || ||||| || ||| |  | ||||| ||||| ||| | ||||||||||| || ||||| || 
-----------------------------cttttgttt----ttccggtaacc--aaacggggttagggtttttttttttttgttttttttgtttttaatt-tcaagataaattgactctgttctgggttttgaagAGCGAGTGACAAGTGCCAGAAGGAGAAGAGGAAGACAATTAATGGTGATGATTTATTATGGGCAATGGCTACGTTAGGGTTTGAAGATTATATTGATCCT

upper sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
lower sequence: EDP06643 (Chlamydomonas reinhardtii), 3'ss of exon 1

gtaagtgcctcag----ctgcggctg------------actcttacttttgcttggcttgttgggaatt-tggagtggcgt----tcagggctttagcttggctggggttt-tgtgttgacttgtccatgtccacgtttttttg-tccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC
||||||| ||  |    | || ||||             | |   |  | ||       ||  |||    | |    ||       || | ||   ||   ||  |  |   ||||  |  |        || | | |  | || |  || || || || || ||||||||||||||| ||||||||||||| || || || |||||||| ||||||||||||||| | ||| |||| ||||| || ||| | || || 
gtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgccgtcaggagcccttgcccagcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgcactatgtagGGCTAGTGACAAGTGCCAGCGGGAGAAGCGGAAAACAATTAACGGCGACGACCTGCTGTGGGCCATGACGACGTTGGGCTTTGAGGAGTACCTGGAGCCG

upper sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1

gtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC
                                                                        | ||  | |||||   ||  | | || |  |   ||   |   | | || | |   ||||||||||| |||||||||||||| || |||||| ||||||| ||||||||||| ||  |||| ||||| |||  ||||||||| || || || ||| | ||||| 
-----------------------------------------------------------------------gtaagtattgctggaagttctt-tcga-tcctttgtggtgatactatcttcttc-tactttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT

upper sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1

gtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC
                                                                        | ||  | |||  | |  | ||| |   |||  |   | |  || || |       ||||| ||||| |||||||||||||| || |||||| ||||||| ||||||||||| ||  |||| ||||| |||  ||||||||| || || || ||| | ||||| 
-----------------------------------------------------------------------gtaagtattgcttcgatcctttgtggtgatgttaa---ctatcttcttcta------ctttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT

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|21809618|gb|BQ667936.1|BQ667936

EST:     GAGACCGTTCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGA                         AGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGA
genomic: GAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGA

EST: gi|18172372|gb|BM347760.1|BM347760

EST:     TGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGA                         AGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGA
genomic: TGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGA

EST: gi|26559930|gb|CA832165.1|CA832165

EST:     GAGACCGTTCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGA                         AGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGA
genomic: GAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGA

EST: gi|161593612|gb|EY964989.1|EY964989

EST:     GAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGA                         AGCGAGTGACAAGT
genomic: GAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGT

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: 153

TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcct ... ctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

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

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 61

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC

           tgttgac  putative branch site (score: 61)
                                 tttttttgtccgctct  putative PPT
                                 tttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttcagggctttagcttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA