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

gtaagtattaggcattcttttggtaccactcatatactggatgtttgatgaaatatatttatccttggtaaacatgtatttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC

Basic information

species	Zea mays
transcript	GRMZM2G081622_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 2

gtaagtattaggcattcttttggtaccactcatatactggatgtttgatgaaatatatttatccttggtaaacatgtatttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC
|||||||| ||    |   ||  |   | |||  | ||| || | | ||||      ||| || | | | | |||||| | | |||||| ||||||||||||||||| ||||| ||||||||||||||||| |||||||| || || ||||| ||||| || ||||| |||||||||||||||||||
gtaagtatcagtttcttaattatt--tattcacttgctgaat-tataatga------tttctcatggatcaccatgtaatct-gcagACAGGAGGCTTTAGTGAGGACATGATTCCTACTGTAGGATTCAACATGAGAAAGGTGACCAAAGGTAATGTCACAATAAAATTGTGGGATCTTGGAGGCC

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G40210.1 (Glycine max), 3'ss of exon 3

gtaagtattaggcattcttttggtaccactcatatactggatgtttgatgaaatatatttatccttggta---aacatgtatttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC---------------------------------
|||||| | |      |   || |   | | || | ||   |  || ||  ||| |  |   | ||  ||   | || |     |   |  |||     |||| ||   || |||| ||    || |||||||||||||| ||||| || ||||| ||||| || |||||||| |||||||||||||| |                                 
gtaagt-tcacttcaccaaatgcttttaattat-tgctttctcctttattcaattttatgggcttttctatctatcaggggcaataatattctgatcaatttattgtt-atctgattccag-

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G05080.1 (Glycine max), 3'ss of exon 3

gtaagt--attaggc---attcttttggtaccactcatatactggatgtttgatgaaatatatttatccttggtaaacatgtatttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC---------------------------------
||||||  | |   |   || |||||  |     |  | | ||  ||      | |   | |||| | |||   ||      | | ||     |||     |||| ||   || |||| ||    || |||||||||||||| ||||| || ||||| ||||| || |||||||| |||||||||||||| |                                 
gtaagttcacttcaccaaatgcttttaattattgttttctcctttattcaattttatggacatttctacttatcaagggcaaaatatt-----ctgacaaatttattgtt-atctgattccag-

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G22480.2 (Glycine max), 3'ss of exon 3

gtaagtattaggc-----attcttttggtaccactcatatactggatgtttgatgaaatatatttatccttggtaaacatgtatttttgcagACTGGAGGCTTTAGTGAGG-ATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC---------------------------------
|||||| |||        |||||||  ||   |    | | |  ||  |   ||| ||  | ||| | |||   || ||      | | | || |   |       || |  || |||| ||    || |||||||||||||| || || || ||||||||||| || |||||||| |||||||||||||| |                                 
gtaagttttatttgccaaattctttcagttatagctttctccatgagttactatgcaaagt-tttctgcttatcaagcaccatagtattctgatttctgatcaatctgtgttatctgattccag-

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0601g00030.t01 (Vitis vinifera), 3'ss of exon 3

gtaagtattaggcattcttttggtaccactcatatactggatgtttgatgaaatatatttatccttggtaaacatgtatttttgcagACTG----GAGGCTTTAGTGAGG-ATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC---------------------------------
           |  || | || | |    |  | ||||   | ||| | ||   |   |  | |||   | || ||| | | ||   | ||    ||   | | |      |  |||||   |  ||||||||||| ||||| ||||| || ||||| ||||| |||||||| ||||||||||||||||| |                                 
---------gtgagttttcttagaaagggttct-tact--ttcttttaggattcaatgtccttcttaacatacctgtttctctgggaagtgatatgaacatatggcattacacttgatcttcag-

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ23242 (Selaginella moellendorffii), 3'ss of exon 3

gtaagtattaggcattcttttggtaccactcatatactggatgtttgatgaaatatatttatccttggtaaacatgtatttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC---------------------------------
                                                |||    |   | | || | |  |  |   || |   |  |||    |||   |          || |    || || ||||| |||||||| ||| | ||||| ||||||||||| ||| | ||||| ||||||||||                                 
-----------------------------------------------gtgagtagtcgattttctcgctggaagttccttctcttacgctg----cttctct-------ctctctcccagGTTGGTTTCAACATGAGAAAGGTTTCTAAAGGCAATGTGACGATCAAGCTATGGGACCTTGGAGGCCAAGCGCGGTTTAGAAGTATGTGGGAGCGATATT

upper sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ25249 (Selaginella moellendorffii), 3'ss of exon 3

gtaagtattaggcattcttttggtaccactcatatactggatgtttgatgaaatatatttatccttggtaaacatgtatttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC---------------------------------
                                                |||    |   | | || | |  |  |   ||||   |  |||    |||   |          || |    || || ||||| |||||||| ||| | ||||| ||||||||||| ||| | ||||| ||||||||||                                 
-----------------------------------------------gtgagtagtcgattttctcgctggaagttccttttcttacgctg----cttctctc---------tctcccagGTTGGTTTCAACATGAGAAAGGTTTCTAAAGGCAATGTGACGATCAAGCTATGGGACCTTGGAGGCCAAGCGCGGTTTAGAAGTATGTGGGAGCGATATT

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|211286502|gb|FL423661.1|FL423661

EST:     TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|9566366|gb|BE475875.1|BE475875

EST:     TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|5296276|gb|AI783046.1|AI783046

EST:     TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|32800459|gb|CD952695.1|CD952695

EST:     TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211212173|gb|FL397456.1|FL397456

EST:     TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211536538|gb|FL409971.1|FL409971

EST:     TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAG
genomic: TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAG

EST: gi|5846813|gb|AI999896.1|AI999896

EST:     AAAACGTCACTTG-GAACTCTATNGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: AAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|149086640|gb|EE176182.2|EE176182

EST:     TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|148949509|gb|EC894973.2|EC894973

EST:     TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|78105314|gb|DV523732.1|DV523732

EST:     TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211135638|gb|FL266964.1|FL266964

EST:     TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|78022902|gb|DV491289.1|DV491289

EST:     AACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: AACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|211184547|gb|FL382110.1|FL382110

EST:     TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

EST: gi|14203624|gb|BG837301.1|BG837301

EST:     TCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGAYCCCTACTGTAGGAWTTCAATATGAG
genomic: TCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGA-TTCAATATGAG

EST: gi|76283087|gb|DV022655.1|DV022655

EST:     TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT                         ACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA
genomic: TGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGA

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), 46 (downstream exon)
Score: 66

CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagtatta ... atttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 73

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 93

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tatactggatgtttgatgaaatatatttatccttggtaaacatgtatttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC

          gtttgat  putative branch site (score: 92)
                                            tattttt  putative PPT
        atgtttgatgaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattaggcattcttttggtaccactcatatactggatgtttgatgaaatatatttatccttggtaaacatgtatttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG