ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacgccccccgtccctcccctccccttctttagtttagatctgcgaacgccgttgtggttggttctgatggtttcgcctgttgcctgccctcccgcctcgaatggggacgggtttgttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC

Basic information

species	Zea mays
transcript	GRMZM2G064563_T03
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 1
lower sequence: EDO98756 (Chlamydomonas reinhardtii), 3'ss of exon 2

gtacgccccccgtccctcccctccccttctttagtttagatctgcgaacgccgttgtggttggttctgatggtttcgcctgttgcctgccctcccgcctcgaatggggacgggtttgttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC
                    || | ||| |||      ||   | |    ||| |||  | |   |   ||   || | || || |   | | | | | ||    |  ||     | ||  |||||||||||||||||| |||||||||||||| ||    || |||   || || ||||  |||                                         
--------------------ctgcgctt-tttgtcgaggacacggggttaccgatgtactggccccc--tgtactcccatgctgaca--cgtgctgacacgtgccgccaccc-cctcttgctgcagCCGGGGACTGGCTTCAGGGCCCCTACGTGTATGCGCTGTACCAGCACTACGGCTATGACGTCAAG-----------------------------------

upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 1

gtacgccccccgtccctcccctccccttctttagtttagatctgcgaacgccgttgtggttggttctgatggtttcgcctgttgcctgccctcccgcctcgaatggggacgggtttgttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC
||  |  |    ||  |  |  || | |     | ||  | || | |   |        |  || ||      |     | ||  ||  | |||| | |              |    ||   |||| || || ||||| ||||| || ||||| |||| |||||||||||| ||||||||| | ||||| || || || || ||||||||||| ||||| |||||
gtgagttctttctcgatttcgcccgcattgcgtgcttccagctcctagatctcgccaaatgcgtactcggatctctagatcttaactctcttccctctttct-----------tcctctcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATGGCTTCCAGAAGGGGGATATTGGGCGGCTCTTCATCGCTGGCTTTGGATC

upper sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ21113 (Selaginella moellendorffii), 3'ss of exon 1

gtacgccccccgtccctcccctccccttctttagtttagatctgcgaacgccgttgtggttggttctgatggtttcgcctgttgcctgccctcccgcctcgaatggggacgggtttgttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC
||  |  |    ||  |  |  || | |     | ||  | || | |   |        |  |  ||      |     | ||  ||  | || | | |              ||   ||   |||| || || ||||| ||||| || ||||| |||| |||||||||||| ||||||||| | ||||| || || || || ||||||||||| ||||| |||||
gtgagttctttctcgatttcgcccgcattgcgtgcttccagctcctagatctcgccaaatgcgcactcggatctctagatcttaactctcttctctctttct-----------ttctctcccccagCGGGAGATTGGCTCCAGGGACCATACGTTTACTTCCTCTACAGCCACTATGGCTTCCAGAAGGGGGATATTGGGCGGCTCTTCATCGCTGGCTTTGGATC

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|149105632|gb|EE291180.2|EE291180

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|211429139|gb|FL408429.1|FL408429

EST:     CTTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|211385926|gb|FL097275.1|FL097275

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|211344703|gb|FL214763.1|FL214763

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|211383298|gb|FL097268.1|FL097268

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|149086869|gb|EE176413.2|EE176413

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|211385929|gb|FL097278.1|FL097278

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGNGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|93012444|gb|EB637964.1|EB637964

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|211344698|gb|FL214758.1|FL214758

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|87156350|gb|DY401139.1|DY401139

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTACG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|101390561|gb|EB817215.1|EB817215

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|211383301|gb|FL097271.1|FL097271

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|211383297|gb|FL097267.1|FL097267

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|211383300|gb|FL097270.1|FL097270

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|148971109|gb|EE021954.2|EE021954

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|149071690|gb|EE160082.2|EE160082

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

EST: gi|211344704|gb|FL214764.1|FL214764

EST:     ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGT                         CCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG
genomic: ATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATG

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: 24 (upstream exon), 40 (downstream exon)
Score: 6

GGGCTCGAGCTCGGCAAGAGCGGCAAGGACCGCGTCGCCACCACCTCCGCATTCAACTCCTTCAAGAACAACTACGTCCTCGTCTACTCCCTCATGATGTgtacgccccc ... gttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC

Block sizes: 47 (upstream exon), 11 (downstream exon)
Score: 4

Block sizes: 28 (upstream exon), 48 (downstream exon)
Score: 5

Block sizes: 47 (upstream exon), 29 (downstream exon)
Score: 8

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtttcgcctgttgcctgccctcccgcctcgaatggggacgggtttgttcgtgcagCCGGGGACTGGCTGCAGGGCCCCTACGTCTACTACCTCTACAGCCAGTATGGCTTCGACAAGGGCGACATCGGCCGCCTCTTCATCGCCGGCTTCGGATC