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

...gctgcaatgttgcaacgagagatggataataatatgcttaacagcctctcctgcattccattgaggttgtcggtttgctgactgaatctcaatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCTGATGATGGCCGCAAACTACCTGGACACTTGATGAGGAGCCTGAGGGATC

Basic information

species	Zea mays
transcript	GRMZM2G000623_T02
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G000623_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 2

gctgcaatgttgcaacgagagatggataataatatgcttaacagcctctcctgcat--tccattgaggttgtcggtttgctgactgaatct-caatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCTGATGATGGCCGCAAACTACCTGGACACTTGATGAGGAGCCTGAGGGATC
     |||||||     | |  |   |      |   ||||    |||   |  |   || | ||| ||     | ||| ||  |   |       ||  |||||| ||||| ||| | |||||||  || ||||| ||||| || ||||||||||||||||| |||||||| |||||||| |||||||  |     |   | 
---caaatgttgttttaatattttacttcattcaaatttaaggcgctcatgtttaacgtcaactgaagtgactcggttgttgttttgtttggttggttgatagTGGGAAGGAGACATCTGAGTTTCAAATTGAACCGGAGATAACTCTGGAGCTGATGATGGCTGCAAACTATCTGGACACCTGATGAGATGAGGTGGAAGTG

upper sequence: GRMZM2G000623_T02 (Zea mays), 3'ss of exon 2
lower sequence: EDO98353 (Chlamydomonas reinhardtii), 3'ss of exon 2

gctgcaatgt-tgcaacgagagatggataataatatgctta-----acagcctctcctgcattccattgaggttgtcggtttgctgactgaatctcaatttc-gtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCTGATGATGGCCGCAAACTACCTGGACACTTGATGAGGAGCCTGAGGGATC
    |||  | ||||   | | | |   |   |  | |  |      |  || |  |  ||| |||   |      |      |   | |  | ||     | | |    |||| | |   | |||||   | | |  || |||||| ||||||||||| | ||||||||||||| ||||||||| |   | |||  |  ||     
----caacttatgcacacacatacgcgcacacaccttcccacccacgcgaccccaaccccatcccacccaccgcaccacccaacctgccgcctgtctcccgcagCACCACCAAGAACATCCCTGAGTTCAAGGTGGCGCCGGAGATCGCCCTGGAGCTGCTCATGGCCGCAAACTTCCTGGACACGTAGGGGGGACACATAGAT---

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|161580201|gb|EY955516.1|EY955516

EST:     ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAG                         TGGCAAGGAAACAGCAGAGTTTCTGATC
genomic: ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAGgttctatgct ... aatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATC

EST: gi|116826509|gb|EC870303.1|EC870303

EST:     ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAG                         TGGCAATGAAACAGCAGAGTTTCTGATCGAACCCGAAATCACCC
genomic: ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAGgttctatgct ... aatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCC

EST: gi|16918633|gb|BM073833.1|BM073833

EST:     ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAG                         TGGCAAGGAAACAGCAAAGTTTCTGATCGAACCCGAGATCACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAGgttctatgct ... aatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCT

EST: gi|18176862|gb|BM351795.1|BM351795

EST:     ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAG                         TGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAGgttctatgct ... aatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCT

EST: gi|18178617|gb|BM379827.1|BM379827

EST:     ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAG                         TGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAGgttctatgct ... aatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCT

EST: gi|32940485|gb|CF045304.1|CF045304

EST:     CTCCATTATTCCAG                         TGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCGCCCTGGAGCT
genomic: CTCCATTATTCCAGgttctatgct ... aatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCT

EST: gi|32940406|gb|CF045225.1|CF045225

EST:     CTCCATTATTCCAG                         TGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCGCCCTGGAGCT
genomic: CTCCATTATTCCAGgttctatgct ... aatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCT

EST: gi|211407289|gb|FL458687.1|FL458687

EST:     ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAG                         TGGCAAGGAGACAGCAGAGTTTCTGATCGAACCCGAGACCACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAGgttctatgct ... aatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCT

EST: gi|60352141|gb|DN219114.1|DN219114

EST:     ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAG                         TGGCAAGGAGACAGCAGAGTTTCCGATCGAACCCGAGATCACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAGgttctatgct ... aatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCT

EST: gi|16926289|gb|BM079357.1|BM079357

EST:     ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAG                         TGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCT
genomic: ATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAGgttctatgct ... aatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCT

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: 45 (upstream exon), 49 (downstream exon)
Score: 45

TCTCCGAGACGCGCCAGGGCGAGGTTCGCTTCCCGGAGATCCCCACCAATATCCTCGAGAAGATCTGCCAGTACTTCTATTGGTCGCTCCATTATTCCAGgttctatgct ... aatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCTGATGATGGCCGCAAACTACCTGGACACTTGATGAGGAGCCTGAGGGATC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 92

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 51

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctctcctgcattccattgaggttgtcggtttgctgactgaatctcaatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCTGATGATGGCCGCAAACTACCTGGACACTTGATGAGGAGCCTGAGGGATC

                              tgctgac  putative branch site (score: 51)
                                           tcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgcaatgttgcaacgagagatggataataatatgcttaacagcctctcctgcattccattgaggttgtcggtttgctgactgaatctcaatttcgtagTGGCAAGGAAACAGCAGAGTTTCTGATCGAACCCGAGATCACCCTGGAGCTGATGATGGCCGCAAACTACCTGGACACTTGATGAGGAGCCTGAGGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
gctgcaa
- - - -tgttgca
- - - - - - - - - - - - - - - - - tgcttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgac