ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcctccagtgcagatcccattggcgcgcgcgaactttgacggtgatggatttatgggtaggggaaggtcggggggtggtgcagccgcgcaggg...

Basic information

species	Zea mays
transcript	GRMZM2G034794_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G034794_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 5'ss of exon 2

CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcctccagtgcagat-cccattggcgcgcgcgaactttgacggtgatggatttatgggtaggggaaggtcggggggtggtgcagccgcgcaggg
|||||| |||||||||||||||||||||||||||||||||||||||||  | ||||| || || |||||||| |||||||||||||||||||||||||||||  | |||| |   | |||||   |  | | || ||||     ||| |||| |    ||    |||  |    |||  |  |   || || |   |    
CGTGCGGTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtt-acctcccctcctccagatgttctcttgtgcccgcggttgatgatggtgttaatgtttgaagtattgatctgtcctgtagaaatggaggcttactttt

upper sequence: GRMZM2G034794_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 5'ss of exon 2

CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcctccagtgcagatcccattggcgcgcgcgaactttgacggtgatggatttatgggtaggggaaggtcggggggtggtgcagccgcgcaggg--
||||||||||||||||||| | ||||||||||||||||||||||||||  | ||||| || || |||||||| ||||||||||||||||||||||||||||| | |  ||| |  | |  |    | || | | | |   |  |     |  ||       || |  |      |||  |   | |   |||  |   |   
CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttcccttc--ttcttactagactgtccccctctctcgctcttactactgtgcccgcggatctgtatcaatcgacgatggatttcgccttggttgctg

upper sequence: GRMZM2G034794_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT4G17390.1 (Arabidopsis thaliana), 5'ss of exon 2

CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcctccagtgcagatcccattggcgcgcgcgaactttgacggtgatggatttatgggtaggggaaggtcggggggtggtgcagccgcgcaggg---
 ||  | || ||||||||  | ||||||||  |||| || || ||     | ||||||||||| |||||||| || || |||||||||||||||||||||||   | || ||   |    ||     |          |    |   ||| |||  ||  ||  |   |     |||   | | |    |    || | |   
GGTTAGGTGTTGGGAGTATCGCCAGCAGCCTTCCATTGTTCGTCTTGTTCGTCCCACTCGTCCCGACAAGGCTCGTCGTCTCGGCTACAAGGCCAAGCAGgtctttttcttcttctcttcattttggttatcaatttaataggtttaggtaatg--ttgttgaatcaagccttatcgattgattgc-tggttaagcggtgtct

upper sequence: GRMZM2G034794_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv00s0551g00020.t01 (Vitis vinifera), 5'ss of exon 2

CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcctccagtgcagatcccattggcgcgcgcgaactttgacggtgatggatttatgggtaggggaaggtcggggggtggt-gcagccgcgcaggg---
 ||  | || ||||||||| | || || ||| |||| || ||  | ||| |||| ||||||||||||||||| ||| |  | ||||||||||| ||||||||| |         ||  || | | ||      || |    ||      || |  || ||   ||| |     |      ||||    | |      | ||   
GGTTAGGTGTTGGGAGTACCGTCAACATCCGTCCATTGTTCGTGTTACACGGCCTACTCGTCCTGACAAGGCTCGCAGATTGGGCTACAAGGCTAAGCAGgta-acaagtggttgtatagttgcaatgcttcagcac---tttcagaattgctttatatactagtatgattgagagaactggtgtccactgatttatatggcac

upper sequence: GRMZM2G034794_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv16s0013g02020.t01 (Vitis vinifera), 5'ss of exon 2

CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcctccagtgcagatcccattggcgcgcgcgaactttgacggtgatggatttatgggtaggggaaggtcggggggtggtgcagccgcgcaggg-
 ||| | |||||||||||  | ||||| ||  | || ||  ||  |||  | |||||||| || || ||||| |||||| | ||||||||||||||||||||     |  |       | ||   |||| ||       | |||     | ||   |  ||  |   |     ||  ||  ||| ||  |       | | 
GGTGAGGTGCTGGGAGTATCGCCAGCACCCTTCAATTGTGTGCGCCACGCGCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAGgttatcattgtttttcttacatttgattg-cgattttttattttattttttatatttgaatttgggcgattgtgttcggttgtgatgatgttcgtttgtgt

upper sequence: GRMZM2G034794_T02 (Zea mays), 5'ss of exon 2
lower sequence: EDP06755 (Chlamydomonas reinhardtii), 5'ss of exon 2

---------CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAG-GCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcctccagtgcagatcccattggcgcgcgcgaactttgacggtgatggatttatgggtaggggaaggtcggggggtggtgcagccgcgcaggg
          |  ||| ||  ||  |||| |    ||| || |  |||   |  |     || |   || |  | |||  ||  || ||||  || ||||||  |||  ||  ||        | ||||| |||  |||     |    |||   ||  || |     ||  | ||   |    |       | ||   || |       
CCCGGACAAGGCCCGCCGCCTGGGCTACAAGGCCAAGCAGGGCTACGTTGTCTACCGCGTGCGCGTCCGCCGCGGCAACCGCAAGCGGCCTGTGC-ACAAGgtaaagtcggcgga--------attgcagctcctcttgattttcc---actcccacaatgctcctgctaatgctaaatgtcactttttttcttgttttgcag-------

upper sequence: GRMZM2G034794_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S28_15V6.1 (Physcomitrella patens), 5'ss of exon 2

CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcctccagtgcagatcccattggcgcgcgc-----gaactttgacggtgatggatttatgggtaggggaaggtcggggggtggtgcagccgcgcaggg
 |||||||||||||||||||||||||  || | ||| |||||| ||||  ||||  |||| ||||||||||| ||  | || || |||||||| ||||| ||   | || |  |    |   |   |||   ||  |     ||   || | |  | | |  || | | |   | |  || | |    |  | |  ||  |||  
TGTGCGCTGCTGGGAGTACAGGCAGCTTCCCGGCATTGTCCGCGTCACTCGGCCTTCTCGGCCTGACAAGGCTCGTAGACTAGGTTACAAGGCTAAGCAAgtgcgtgtcattaaaccgattacttcttgttacgttcatgtggatactttatgtcgtttg--ttgtagttgcagtactgttgtgcctggaggtactcgt-cag--

upper sequence: GRMZM2G034794_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S68_114V6.1 (Physcomitrella patens), 5'ss of exon 2

CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcctccagtgcagatcccattggcgcgcgcgaactttgacggtgatggatttatgggta--ggggaaggtcggggggtggtgcagccgcgcaggg
 ||||| |||||||||||||||||||  || |  ||||||||| ||||  | ||  |||||||||||||||| ||||| || || |||||||||||||||||     | |     | || ||   | ||  |  |  ||  | ||    |  | | ||  |   |      | || |       |  |  |     | ||||
TGTGCGATGCTGGGAGTACAGGCAGCTCCCAGGAATCGTCCGCGTCACTCGCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtg--ctttcatggatccatatgtaactgttgtaccagatttgtggaacttgtaggttcttccatttcacaggagatatttaaattttaaaaagttggaggg

upper sequence: GRMZM2G034794_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S152_141V6.1 (Physcomitrella patens), 5'ss of exon 2

CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcctccagtgcagatcccattggcgcgcgcgaactttgacggtgatggat-ttatgggtaggggaaggtcggggggtggtgcagccgcgcaggg-
 |||||||||||||||||||||||||  || | ||| |||||  ||||  | || |  ||||| |||||||| |||||||| || || ||||||||||||||     | |  | |      ||   ||  ||  ||  | |  |||  |     | | || | ||  | |    ||  |   ||   | ||    |    | 
TGTGCGCTGCTGGGAGTACAGGCAGCTCCCCGGCATTGTCCGTGTCACTCGCCCTAGCCGTCCCGACAAGGCTCGCCGCCTAGGGTATAAGGCCAAGCAGgtcagcttgcatctgaatctttcgagttttcgt-cgaaagccatgaaagaatctgttcttgtaggctgcgtggagt-agcttgtttcgaagttaggatttga

upper sequence: GRMZM2G034794_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S134_151V6.1 (Physcomitrella patens), 5'ss of exon 2

CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcctccagtgcagatcccattggcgcgcgcgaactttgacggtgatggatt-tatgggtaggggaaggtcggggggtggtgcagccgcgcaggg-----
 || |||||||||||||||||||||| ||| | ||| |||||| ||||  | || |  || ||||||||||| ||||| || || |||||||||||||||||   | |      |   |||  || ||||     | |   |||| | || || | || | || ||         ||     |    || | |  | |        
TGTTCGCTGCTGGGAGTACAGGCAGCTGCCCGGCATTGTCCGCGTCACCCGCCCTAGCCGCCCTGACAAGGCTCGCCGTCTTGGTTACAAGGCCAAGCAGgtcagttt-----ggattagagacccttggtttcagtgt-ttttgtctgtaattgtttctgtgtgtctacatttatctacatggaacgctgtcttggacattaggg

upper sequence: GRMZM2G034794_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S34_445V6.1 (Physcomitrella patens), 5'ss of exon 2

CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctc----ctccagtgcagatcccattggcgcgcgcgaactttgacggtgatggatttatgggtaggggaaggtcggggggtggtgcagccgcgcaggg-
 |||||||||||||||||||||||||  || | |||||||||| ||||  | ||  |||| ||||||||||| ||||| || || ||||||||||||||||||  | |     || || |   |   | |||  |  || |   |||||    ||    | || | |     | |  ||   |  |  |||  |    |  | | 
TGTGCGCTGCTGGGAGTACAGGCAGCTCCCCGGCATCGTCCGCGTCACTCGCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttgagacttcaatttgg---ctattttcttgcacc--ctttgcatttggaaaaattgtagcatttgaattgttttgatggcgtggcgtgaagtggcgt

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|9028655|gb|BE238695.1|BE238695

EST:     GGCCCACTCGCCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAG                         GCGTGGTGGCAGGAAGAGGCCTGTGCCTAAAGGTATTGTCTATGGCAAGCC
genomic: GGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcc ... tccgtgttagGCGTGGTGGCAGGAAGAGGCCTGTGCCTAAAGGTATTGTCTATGGCAAGCC

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: 17

CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcc ... tccgtgttagGCGTGGTGGCAGGAAGAGGCCTGTGCCTAAAGGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCCAGCTCAAGTTCCAGAGGAACAAGAGGTCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 17

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 4