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

...ttcattttctaaaattagttcatttttacttgaaaaatgagaatcctttggaaaaatggagttaccaaactagcctaataaaatttatttatatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCATATAGTGGTGGTCTAGGAGGAATATCGTTTGATGGTGACATGCAAATTG

Basic information

species	Zea mays
transcript	GRMZM2G161337_T03
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G161337_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G03260.1 (Glycine max), 3'ss of exon 10

-----------------------------------------------------------ttcattttctaaaattagttcatttttacttgaaaaatgag-aatcctttggaaaaatggagttaccaaactagcctaataaaattta-----------------tttatatgac----cagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCATATAGTGGTGGTCTAGGAGGAATATCGTTTGATGGTGACATGCAAATTG
                                                           ||    ||  ||||||    | || ||     | |  | |   | | |||    | |   ||     ||| || | |   |||| ||                  ||||| ||      ||||||||||| ||||||||||||||| | ||||| ||||  ||||||||||| |||||||| ||  | |||   || || ||   |||||| ||| | ||||
gtttgtaattttcttgactcctttttagtcaacttagacaaaacattttatgttttcgcttttaattacaaaattgtcgccttgttttcaaataggtaaacgaacttttaattacagaaagcagtgaaaataacttttcaaaacttgccaccttgattcgttcttttatgtggatatgcagGTGAAGGCAATGGAGTTGATTGATGAATTGGAGGTTAAAAGGCGAGGACCTTATAGTGGAGGATTTGGATACATCTCTTTCCTTGGTGAGATGGACATTG

upper sequence: GRMZM2G161337_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g06320.t01 (Vitis vinifera), 3'ss of exon 10

---------------------------------------------------------------------------------------------ttcatttt--ctaaaattagttcatttttacttgaaaaatgagaatcctttg--gaaaaatggagttaccaaactagcctaataaaatttatttatatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCATATAGTGGTGGTCTAGGAGGAATATCGTTTGATGGTGACATGCAAATTG
                                                                                             | |||     ||   |  ||| |  |  | | |||   |||    |  |||   ||         |||      |  | |  | |  | |  |   ||   ||||||||||||||||||||||||||| || ||||||| || ||||| || ||||||||||||||| | || ||||| || |||   ||||| ||| | ||||
gtatgcacgcaccaaccgccttccttctctaattacacatttgtggtgtctggttgtttgtggtcctgagttgtgaggaaataaattgtcaagtccatccaggctttcacgagtacgctaatgcatgatctatgtacctgttttcatgagggtccattttatgtcgatgacattgtcagctctgctacaata--cagGTGAAGGCCATGGAGTTGATTGATCAGCTGGAAGTCACAAGGCGTGGGCCATATAGTGGTGGTTTCGGGGGAATTTCCTTTTCGGGTGATATGGACATTG

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|7227817|gb|AW566458.1|AW566458

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|71762476|gb|DR960413.1|DR960413

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|211345790|gb|FL266263.1|FL266263

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|149103558|gb|EE288957.2|EE288957

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|8930541|gb|BE225305.1|BE225305

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|4887265|gb|AI677364.1|AI677364

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|37392136|gb|CF633315.1|CF633315

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|211345792|gb|FL266265.1|FL266265

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|548048|gb|T25248.1|T25248

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|71761802|gb|DR959739.1|DR959739

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|60357763|gb|DN224736.1|DN224736

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|213175359|gb|FM190077.1|FM190077

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|148939087|gb|EC883495.2|EC883495

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|60398523|gb|DN231339.1|DN231339

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|149000181|gb|EE037320.2|EE037320

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|5713996|gb|AI943981.1|AI943981

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|13178556|gb|BG349814.1|BG349814

EST:     ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

EST: gi|94476712|gb|EB705670.1|EB705670

EST:     ATGCCTTGAGAGCTGCCTTCCCCGTTGGAACAGTCAGTGGTGCCCCAAAG                         GTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA
genomic: ATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCA

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: 205

GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgt ... atatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCATATAGTGGTGGTCTAGGAGGAATATCGTTTGATGGTGACATGCAAATTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 704

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1088

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctttggaaaaatggagttaccaaactagcctaataaaatttatttatatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCATATAGTGGTGGTCTAGGAGGAATATCGTTTGATGGTGACATGCAAATTG

                           gcctaat  putative branch site (score: 206)
                     aaactagcctaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcattttctaaaattagttcatttttacttgaaaaatgagaatcctttggaaaaatggagttaccaaactagcctaataaaatttatttatatgaccagGTGAAGGCCATGGAGTTGATTGATAAGTTGGAAGTTACGAGGCGAGGACCATATAGTGGTGGTCTAGGAGGAATATCGTTTGATGGTGACATGCAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA