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

gttcggctcatgttttttgtgctcttttgccactggtaggtgttttttttggtaagtgatcattctgcttacataagtgtgatttttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA

Basic information

species	Zea mays
transcript	GRMZM2G114793_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 5

gttcggctc--atgttttttgtgctcttttgccactggtaggtgttttttttggtaagtgatcattctgcttacataagtgtgatttttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
||||| |    ||    |   |  || ||||    |||||     |    |   |  ||  |   | | ||||      | ||||||| |     | ||||||||||| ||||| |||||||| ||||| ||||| ||||||||||| ||||||||||||||||||||||||||||| |||||||| |||||||| |||||
gttcgaccttgatcacatacatagtcctttgg-gttggtaacaactgcgatca-tctgtcttgcatatacttatcgtgctttgattttggt----acgcagATATCCTTCTCCTGGATGTGGCACCCCTTACCCTCGGTATCGAGACTGTCGGTGGAGTCATGACCAAGTTGATCCCCAGGAACACCGTCATCCCCACCAA

upper sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 5

--------gttcggctcatgttttttgtgctcttttgcc---actggtaggtgttttttttggtaagtgatcattctgcttacataagtgtgatttttgccttg--------atgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
        ||  |     |   ||||    |  ||  ||   | |  ||  | || |||  |  |   |||   |  || ||      | | ||  |||  | |        || |||| ||||| ||||| ||||||||||||||||| || || || || || || |||||||||||||| |||||||| || || |||||||| ||||| |||||
gtaccgtagtctgtaatgtagcttttaaattacttgtcccgaagtcataaatattatttacgcaattagattgctaagcataacactttctaatcgttgtgtggcaatatctatccagACATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCAACCAA

upper sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 5

gttcggctcatgttttttgtgctcttttgccactggtaggtgttttttttggtaagtgatcattctgcttacataagtgtgattt--ttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
                 |    |  | ||  | |  ||  | |     | | |   | | ||||   ||| | ||| |||  | |      ||  || |||||||||| ||||| ||||||||||||||||| || || || || || || |||||||||||||| |||||||| || || |||||||| |||||||||||
----------------gtaccatagtctgtaaatattatttatggaagtagattgctaagcattacactttc-taattgttgtgtggcaatctctatccagATATCCTTCTCCTGGATGTGGCTCCCCTCACTCTCGGAATTGAAACTGTTGGTGGAGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAA

upper sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 5

-----------gttcggctcatgttttttgtgctcttttgccactggtaggtgttttttttg---gtaagtgat----cattctgct--tacataagtgtgatttttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
             |   || |  | |    | ||  |     | |  ||  | || ||| ||   |||  |  |    ||||  |||    |||   |||| |   |  || ||| |||||||||| ||| | |||||||||||||||||||| || || || || || ||||| || ||||| |||||||| || || |||||||| ||||| |||||
gtactgtagtctgtaatctaacttctcaattacttgtccagaaatcataaatattatttatgcaagtagattgtgacacattacgctgtctcattgttgtg-tggctctctggatccagATATCCTTCTCTTGGATGTGGCTCCCCTCACCCTTGGAATTGAAACTGTTGGTGGGGTGATGACGAAGTTGATTCCCAGAAACACTGTTATCCCTACCAA

upper sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 5

----------gttcggctcatgttttttgtgctcttttgccactggtaggtgttttttttggtaagtgatcattctgc-ttaca-----taagtgtgattt--ttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
           |       |  || |   | ||  |     | |  ||  | || ||| ||  |   |||      || |||||     | | |||  | |   |  || ||| |||||||||| ||| | |||||||||||||||||||| || || || || || ||||| || ||||| |||||||| || || |||||||| ||||| |||||
gtactacagtctgtaatctaacttctcattacttgtccagaaatcctaaatattatttatgcaagtagattgccacgcattacactttctcattgttgtgtggctctctggatccagATATCCTTCTCTTGGATGTGGCTCCCCTCACCCTTGGAATTGAAACTGTTGGTGGGGTGATGACGAAGTTGATTCCCAGAAACACTGTTATCCCTACCAA

upper sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 5

gttcggctcatgttttttgtgctcttttgcc-actggtaggtgttttttttggtaagtgatcattctgcttacata---agtgtgatttttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
         ||  |||   | |||| |     || | ||| || || |       |||| | ||      || | |     | |||| ||||     |||||||||| || ||| | ||||||||||| ||||| || || || || ||||| ||||| || |||||||||||||| || ||||||||||| |||||||||||
-------gtatcatttccattctctatcaatgaccgatagatggttgtgc-atcgagtgttgatgaatggtagacatttgatatgatatttgttcc-atgcagATATTCTTCTCTTGGATGTGGCTCCGCTCACTCTTGGAATTGAAACCGTTGGTGGGGTGATGACCAAGTTGATTCCTAGGAACACTGTTATCCCGACCAA

upper sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ29073 (Selaginella moellendorffii), 3'ss of exon 5

gttcggctcatgttttttgtgctcttttgccactggtaggtgttttttttggtaagtgatcattctgcttacataagtgtgatttttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
                                   | |     || | ||  |  || |||  ||||  | |  | | | |    | |        |||  || || ||| | || || || ||||| || ||||||||||||||||| |||||||| ||||||||| ||||||| |||||||||||||| ||||||||
-------------------------------gtaagcaaagacttgtcttcttttgtaatccatctg--tgctaacgcgcgtccatcg-------acagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTGGTGGAGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAA

upper sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ17607 (Selaginella moellendorffii), 3'ss of exon 5

gttcggctcatgttttttgtgctcttttgccactggtaggtgttttttttggtaagtgatcattctgcttacataagtgtgatttttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA
                                   | |  |  || | ||  |  || ||   ||||  | |  | | | |    |||        |||  || || ||| | || || || ||||| || ||||||||||||||||| |||||||| ||||||||| ||||||| |||||||| ||||| ||||||||
-------------------------------gtaagcaaatacttgtcttcttttgtaattcatctg--tgctaacgcgcgtccattg-------acagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTGGTGGAGTGATGACCAAGCTGATCCCCAGGAACACGGTCATTCCGACCAA

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|67021339|gb|CO450088.1|CO450088

EST:     CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAG                         ATATCCTCCTCCTTGATGTGGCTCCCTTCACCCTGGGTATCGAGACCGTCG
genomic: CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAGgttcggctca ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCG

EST: gi|5343005|gb|AI795310.1|AI795310

EST:     CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAG                         ATATCCTCCTCCTTGATGTGGNCTCCCCTCACCCTGGGTATCGAGACCGTC
genomic: CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAGgttcggctca ... cttgatgcagATATCCTCCTCCTTGATGTGG-CTCCCCTCACCCTGGGTATCGAGACCGTC

EST: gi|19822640|gb|BQ048664.1|BQ048664

EST:     CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAG                         ATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCG
genomic: CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAGgttcggctca ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCG

EST: gi|18450481|gb|BM428759.1|BM428759

EST:     CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAG                         ATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCG
genomic: CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAGgttcggctca ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCG

EST: gi|67028334|gb|CO457083.1|CO457083

EST:     CGCTGTGCAGGAAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAG                         ATATCCTCCTCCCTGATGTGGCTCCCCTCACCCTGNGTATCGAGACCCGTC
genomic: CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAGgttcggctca ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACC-GTC

EST: gi|67029818|gb|CO458567.1|CO458567

EST:     CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAG                         ATATCCNTCCTCCTTGATGTGGCTCCCCTCACCCTGNGTATCGAGACCGTC
genomic: CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAGgttcggctca ... cttgatgcagATATCC-TCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTC

EST: gi|20803248|gb|BQ294298.1|BQ294298

EST:     CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAG                         ATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCG
genomic: CGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAGgttcggctca ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCG

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: 158

AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAGgttcggctca ... cttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 464

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttttttggtaagtgatcattctgcttacataagtgtgatttttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA

                                      tttttgcctt  CT-rich tract
                        ttacataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcggctcatgttttttgtgctcttttgccactggtaggtgttttttttggtaagtgatcattctgcttacataagtgtgatttttgccttgatgcagATATCCTCCTCCTTGATGTGGCTCCCCTCACCCTGGGTATCGAGACCGTCGGTGGAGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG