ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtaattcacatacccccaccctcgccgtctaccgtgcgtgtggcctttcctatgcactattcttacacatctttcactgatttcattacccatttctgctttcttggcgttgtttggactatggaagGTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGCAGACCTCCGCTCGTTCAGCGACGGTTCAACAAGCCTCTTCTTCCAGCTA

Basic information

species	Zea mays
transcript	GRMZM2G141216_T01
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G141216_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g07390.1 (Oryza sativa), 3'ss of exon 7

gtaa-ttcacatacccc-caccctcgccgtctaccgtgcgtgtggcctttcctatgcactattcttacacatctttcactgatttcattacccat--ttctgctttcttggcgttgtttgg--actatggaagGTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGCAGACCTCCGCTCGTTCAGCGACGGTTCAACAAGCCTCTTCTTCCAGCTA
|||| | ||  || |   |||||||  | |||| |   |        |||| ||     | | ||    ||||||| || ||| ||||     ||  ||      || |  |    ||     || |||| ||||||||||||||||| || |||||||| ||||| || |||||||| |||||||||||||| |||||| | || || ||||| |||||||| |||||||||
gtaagtacatgtatcttgcaccctcttcttctagc---cactgaaaatttcttaa----tttcctcgtgcatcttttaccgatctcatgcttaatgctttcaacctcataccaaccttgaacaacaatggcagGTTCGAGAGGGAGCGGACATGCCCGCTATGCAGAGCGTTGGTGAAACCAGCAGACCTCCGGTCGTTCGGTGATGGCTCAACGAGCCTCTTTTTCCAGCTA

upper sequence: GRMZM2G141216_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S22_135V6.1 (Physcomitrella patens), 3'ss of exon 7

------------------------------------------------------------gtaattcacatacccccaccctcgccgtctaccgtgcgtgtggcctttcctatgcactat-tcttacacatctttcactgatttcattacccatttctgctttcttggcgttgtttggactatggaagGTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGCAGACCTCCGCTCGTTCAGCGACGGTTCAACAAGCCTCTTCTTCCAGCTA
                                                            |||      ||          | |    |    ||  | | ||  ||   |||| |  |  |  ||    |       |||              |   | || |  |||| || | |  | ||| ||||||||||||||||||||||| ||| ||||| ||||  | ||||| || | ||  || || ||||   | ||||| || || ||||| ||| ||||| | 
gtgagttgggtggcattgcagttggtggttaggatggggggtgggatgggagggagggaggtaggagggatggatgggtgtttgtg--cggttgtttgagcggtgttgtgtatgaagaagatggtatgggtgggg-gttgaggaggagcgatgcgtgaacgttgtgtgcgtggtgttggat-tggcagGTTCGAGAGGGAGCGAACGTGTCCGTTGTGCCGGGCCGTAGTGAAACCGGTAGGTCTGCGGTCGTATGGGGACGGATCGACGAGCCTGTTCATCCAGTTG

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|37401093|gb|CF637909.1|CF637909

EST:     ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATG                         GTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGC
genomic: ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATGgtaattcaca ... actatggaagGTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGC

EST: gi|67013572|gb|CO442321.1|CO442321

EST:     ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATG                         GTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGC
genomic: ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATGgtaattcaca ... actatggaagGTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGC

EST: gi|37361112|gb|CF602401.1|CF602401

EST:     ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATG                         GTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGC
genomic: ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATGgtaattcaca ... actatggaagGTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGC

EST: gi|37378364|gb|CF625868.1|CF625868

EST:     ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATG                         GTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGC
genomic: ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATGgtaattcaca ... actatggaagGTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGC

EST: gi|211149831|gb|FL250219.1|FL250219

EST:     ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATG                         GTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGC-AGC
genomic: ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATGgtaattcaca ... actatggaagGTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGC

EST: gi|40334853|gb|CK368923.1|CK368923

EST:     ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATG                         GTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGC
genomic: ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATGgtaattcaca ... actatggaagGTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGC

EST: gi|211105992|gb|FL446094.1|FL446094

EST:     ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATG                         GTTCGAGAGGGAGCGAACGTGCCCGCTGTGTAGGGCATTGGTGAAGCCAGC
genomic: ATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATGgtaattcaca ... actatggaagGTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGC

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: 47 (upstream exon), 46 (downstream exon)
Score: 30

TTGCTGCTGGAGACTTGTGTGCGATATGCCAAGAAAAGATGCATGTTCCCATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCGAATGgtaattcaca ... actatggaagGTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGCAGACCTCCGCTCGTTCAGCGACGGTTCAACAAGCCTCTTCTTCCAGCTA

Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 57

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 66

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 128

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttcactgatttcattacccatttctgctttcttggcgttgtttggactatggaagGTTCGAGAGGGAGCGAACGTGCCCGCTGTGCAGGGCATTGGTGAAGCCAGCAGACCTCCGCTCGTTCAGCGACGGTTCAACAAGCCTCTTCTTCCAGCTA