ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...tcttaactatatgatggtactatcttctaatgcccacttatatgtgtcaccctgacatttttctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG

Basic information

species	Zea mays
transcript	GRMZM2G110983_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 3'ss of exon 4

---------------------tcttaactatatgatggtactatcttctaatgcccacttatatgt-gtcaccctgacatttttct-----catatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
                     | |  ||  ||  || | |  || || |  |  |  | | | | |      ||| ||||||| ||     ||| | |||||||||||||||| ||||||||||||||||| || || || |||||||| || ||||||||||||||||| |||||||| || ||||||
tgctacttgtgtggaagcacttatgtaccttagaatagcatgatattgttgtatctccatttgttttactttcctaacattttccttttatcatgtacagTTTATGCTGATGGGAGCATATGCTTAGATATACTACAAAACCAGTGGAGCCCCATATATGATGTAGCTGCTATACTCACATCCATCCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G05080.1 (Glycine max), 3'ss of exon 4

--------------tcttaactatatga----tggtactatcttctaatgccca---------cttatatgtgtcaccctgacatttttctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
                  | || ||||       ||||||| ||||  || | |         |||  |  | | | ||     |  || |||  |  ||||||||| |||||||||||||| || || ||  | || ||||| ||||||||||| |||||||| ||||| ||||| || ||||| |||
ctttctatggatcaatgaatctgtatggaaatcagtactattttcttttgtcaagtaaggtaacttccagttctgagccccttttccttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGTCCGATTTATGATGTTGCTGCAATACTTACCTCAATTCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G16160.1 (Glycine max), 3'ss of exon 5

---------tcttaactatatgatggtactatcttctaa-----tgcccacttatatgtgtcaccctgacatt------tttctcatatg-------cagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
         | | || | |   |    || || || ||      |||   || |||  | | |  |||    |       |  | |  ||        ||||||||| ||||| || |||||||| || ||  | |||||||||||||| || || ||||| |||||||| || || || |||||||||
ctatgttaatttaaattgtggtacaaaacaattttgtatatgtttgcatgctaatacctttgaatctggttctaagcccctctttacttggaaattttagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAGAATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G34170.2 (Glycine max), 3'ss of exon 4

tcttaactatatgatggta-----ctatcttctaatgcccac----ttatatgtgtcaccctga--catttttctcat---atgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
   ||| |||  | ||| |      ||  ||  | |  | |     |||  |||||  | || |  |||||||   |     || |||||||||||||||||| || || || ||||| || || |||||||||||||| ||||||||||| ||||| |||||||| || ||||||
--gtaagtattaggtggaaaatctttacgttggagtatcaataaatttagctgtgtagctctaattcattttttcaacttcgtgtagTTTATGCTGATGGAAGTATTTGTTTGGATATACTACAAAATCAGTGGAGTCCTATATATGATGTGGCTGCTATACTCACATCTATCCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G02400.2 (Glycine max), 3'ss of exon 4

---------------tcttaactatatgat--ggtactatcttctaatgcccacttatatg---tgtcaccctgacatttttctcatatgc-------agtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG-----------
                   || ||  | ||   ||||||| | ||  || | | ||   |    ||     ||||     || || | ||        ||||||||| |||||||||||||| || || ||  | || ||||| ||||| ||||| |||||||| || |||||||| || ||||| |||           
gattaatgaatctgtatggaaataagtaattaagtactatttgcttttgtcaagttcggtaatttgcagttctgagccccttttcctttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGGTCATAGTGAT

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G01270.1 (Glycine max), 3'ss of exon 4

-----tcttaactatatgatggtactatcttctaatgc-----ccacttatatgtgtcaccctgacatttttctcatat--gcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
     | |||  |  |  |   ||  ||||||  || |       || ||| |   |     || |||||||||  | |  | ||||||||| |||||||| || || || |||||  | || || ||||||||||| ||||||||||||||||| |||||||| || ||||||
gtaagttttaggtggaaaagatta--atcttcctatccgtaaattacctatgtagctactaatgtcatttttctactcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G02400.1 (Glycine max), 3'ss of exon 4

---------------tcttaactatatgat--ggtactatcttctaatgcccacttatatg---tgtcaccctgacatttttctcatatgc-------agtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
                   || ||  | ||   ||||||| | ||  || | | ||   |    ||     ||||     || || | ||        ||||||||| |||||||||||||| || || ||  | || ||||| ||||| ||||| |||||||| || |||||||| || ||||| |||
gattaatgaatctgtatggaaataagtaattaagtactatttgcttttgtcaagttcggtaatttgcagttctgagccccttttcctttgtcaattttagTTTATGCAGATGGAAGCATATGTTTGGACATTTTACAAAATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G10640.1 (Glycine max), 3'ss of exon 4

-----tcttaactatatgatggtactatct---tctaatgcccacttatatgtgtcaccctgacatttttctcatatgc--agtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
     | |||  |  |  |   || | |     || |      || ||| |   |     || |||||||||  | ||   ||||||||| |||||||| || || || |||||  | || || ||||||||||| ||||||||||||||||| |||||||| || ||||||
gtaagttttaggtggaaaagattaatcttcatgtccataaattacctatgtagctactaatgccatttttctactctgggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G40860.1 (Glycine max), 3'ss of exon 4

------------------------tcttaactatatgatggtactatcttctaatgcccacttatatgtgtc---accctgacatttttctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
                         |  ||| || |  |     |     ||| |  |     || |   ||    |||     |  ||  ||  |  ||||||||| ||||| || |||||||| || ||  | || ||||||||||| || ||||||||||||||||| || || || |||||||||
tcctgtgttaatttaaattggagtacaaaacaattttgtatctttgcacgctagtaactttgaatctagttctaagcccctctttacttggcaattatagTTTATGCGGATGGCAGTATATGCTTGGACATTTTACAAAATCAGTGGAGCCCTATATATGATGTAGCTGCAATTCTTACCTCAATCCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G16160.3 (Glycine max), 3'ss of exon 4

--------tcttaactatatgatggtactatcttctaa-----tgcccacttatatgtgtcaccctgacatt------tttctcatatg-------cagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG-
        | | || | |   |    || || || ||      |||   || |||  | | |  |||    |       |  | |  ||        ||||||||| ||||| || |||||||| || ||  | |||||||||||||| || || ||||| |||||||| || || || ||||||||| 
tatgttaatttaaattgtggtacaaaacaattttgtatatgtttgcatgctaatacctttgaatctggttctaagcccctctttacttggaaattttagtTTATGCGGATGGCAGTATATGCTTGGACATTTTACAGAATCAGTGGAGCCCTATTTATGACGTAGCTGCAATTCTTACCTCAATCCAGG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G20310.1 (Glycine max), 3'ss of exon 3

-----tcttaactatatgatggta-----ctatcttctaatgcccac---ttatatgtgtcaccctga--catttttc-----tcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
     | ||   |  |   ||| |      || |||  | |  | |    |||  |||||  | || |  |||||||      |  | || |||||||||||||||||| || || || |||||  | || |||||||||||||| || |||||||| ||||| |||||||| || ||||||
gtaagtattgggtggaaattggaaaatctttaccttggagtatcaataaattagctgtgtagctctaattcattttttcaactttgtgtgtagTTTATGCTGATGGAAGTATTTGTTTGGATATATTACAAAATCAGTGGAGTCCTATTTATGATGTGGCTGCTATACTCACATCTATCCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G62540.1 (Arabidopsis thaliana), 3'ss of exon 4

----tcttaactatatgatggtactatcttctaatg--cccacttatatgtgtcaccctgacattttt-ctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
     |  ||  ||    ||  || |  |  ||||   || | |   |  |   ||  ||| | ||   ||    |||||||||||||||||||||||| ||||| |||||| |||| || |||||||| || || || || || |||||  | ||||| ||||| |||
gtaagcccaagcattcagtga-acaacatagtaatagaccaattaggaaattcgactttgataattgaactttggtgcagTTTATGCTGATGGAAGCATTTGCTTGGATATCTTGCAAAACCAGTGGAGCCCCATCTACGACGTTGCTGCAGTTCTCACATCAATTCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT2G02760.1 (Arabidopsis thaliana), 3'ss of exon 4

------tcttaactatatgatggtactatcttctaatgcccacttatatgtgtc--accctgacatttttctcatat---gcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
      |    | |||   ||  || | ||||    ||   || | |      |  |  || ||| ||     || |   ||||||||||||||||| || |||||||| || || || || || || |||||||| ||||| ||||| ||||| ||||| || || || |||
gtaagttggagattatcacatcatagtttcttactctgagtacatgtgatcaacgaaagctcacacttggtcaatgttgtgcagTTTATGCTGATGGGAGTATATGCTTGGACATTCTCCAAAACCAATGGAGTCCAATATACGATGTCGCTGCTATACTAACCTCCATTCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 3'ss of exon 5

-----------------------tcttaactatat-gatggtactatcttc--taatgcccacttatatgtgtcaccctgacatttttctcatatg-cagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
                       | ||| || | | || |  ||||   |   || |       | |   || | |   |   | ||  || | || |||||||||| ||||||||||| |||||||| || || || |||||||||||||| || |||||||||||||| ||||| || || ||||||
catgatgatgatcatcataatgtttttagcttttttgaggaaactaaactaagtattattttgctgttgctggctctaagttctcttaatcttttgtcagTTTATGCGGATGGAAGCATTTGCTTAGACATTCTACAAAATCAGTGGAGTCCAATTTATGATGTAGCTGCCATACTTACATCCATCCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 5

-------------------------tcttaactata-tgatggtactatcttctaatgccca-cttatatgtgtcaccctgacatttttctcat--atgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
                         |||   || |  |||      ||  |  |  ||  || || |||   ||   ||||| ||||||    |  |  |||| ||||| ||||||||||| || || ||||| || ||||| ||||||||||| ||||||||||| ||||| || || || || ||||||
ctaccccttttattttttaatatattctgttctctggtgagaaatgtaattaatggtgtgcagctcataatagtt--cctgatatttttgcttttgaatcagTATATGCCGATGGAAGCATCTGTTTGGATATTCTACAGAACCAGTGGAGTCCCATATATGATGTTGCTGCTATTCTTACTTCTATCCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 4

-----tcttaactatatga----tggtactatcttct----aatgcccacttatatgtg-----tcaccctgacatttt-tctcatatg---cagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
     |   |||||| |      | |||  |  |  |    |||      |||  || |     | ||    || |||| | |   ||    |||| ||||| |||||||| || ||  | ||||| || || |||||||||||||| |||||||||||||| || ||||| ||||| || |||
gtaagttggaactatgttgcaattagtatcacttcatgttaaatatttctttagctgcggtttcttacttctaccttttattttgaattggccagTCTATGCAGATGGAAGTATTTGTCTCGATATTCTACAAAATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0032g00310.t01 (Vitis vinifera), 3'ss of exon 3

-------------------------------------------------------------------------------------------tcttaa-ctatatgatggtactatct-tctaatgcccacttatatgtgtcacc-ctgacatttttctcatatg------cagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
                                                                                           | |||  || || ||   ||||| |  | |  |  |||| |     | | | | |||||    ||   ||  |      |||||||||| |||||||| || ||||| |||||  | ||||||||||||||||| ||||||||||| || || |||||||| || ||||||
gtatgtcacaatcctattcttgaattgcattcctggttatgcaatatagatcataaactgcttatgcgaatgtttctttttggcatctatctattactctctaggactatactaacaatgttgtttccacattagcatctaatctctgactgcatttgtatgggtttgatcagTTTATGCAGATGGAAGTATTTGCTTGGATATTTTACAGAATCAGTGGAGTCCTATATATGATGTGGCAGCTATACTCACTTCCATCCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 3'ss of exon 3

-----------------------------tcttaactatatgatggtactatcttctaatgcccacttatatgtgtcaccctgacatttttctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
                              | |     |      | |         |  || |   | | ||| | |  | |   | ||| |   |  |||| ||||| || || ||||| ||||||||||||||||| ||||||||||| ||||| || || || || |||||  | || || || |||
ctagcgcttgtgttgaggacgtttggagtccctgggcgtggagccg-agagggacacagcgcgcgtctctgtgt-ttatgcggtggtgtttgtggcaaacagTATATGCGGACGGTAGCATCTGCTTAGATATCCTGCAAAATCAGTGGAGCCCGATCTACGACGTGGCAGCGATTTTGACTTCGATTCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ17802 (Selaginella moellendorffii), 3'ss of exon 3

tcttaactatatgatggtactatcttctaatgcccacttatatgtgtcaccctgacatttttctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
                ||     | | |  |      |||  | | |     |   | |  |||  | ||||||||||||||||||||| || ||| | || || ||||| ||||| ||||||||||| || ||||| || || || || ||||| || |||
----------------gtgagtccctttcttctttctttaattttctttttttcttactcatctttt-tgcagTTTATGCTGATGGAAGTATTTGCCTCGACATACTGCAAAATCAATGGAGTCCGATCTACGATGTTGCGGCAATTCTTACGTCCATACAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ21576 (Selaginella moellendorffii), 3'ss of exon 3

tcttaactatatgatggtactatcttctaatgcccacttatatgtgtcaccctgacatttttctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
                    ||  |||   |   |  |  | | | ||  ||| ||    |        ||||||||||| ||||||||||| ||  | || ||||| || ||||||||||| ||||| |||||||| || || ||||| || || ||||||
-------------------gtaagttcgtttattcg-tagtgtctatcttccttacgcgctctc-----gcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATCTATGATGTTGCCGCAATACTGACATCGATCCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ23951 (Selaginella moellendorffii), 3'ss of exon 3

tcttaactatatgatggtactatcttctaatgcccacttatatgtgtcaccctgacatttttctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
                    ||  |||   |   |  |  | | | ||  ||| ||    |        ||||||||||| ||||||||||| ||  | || ||||| || ||||||||||| ||||| |||||||| || || ||||| || || ||||||
-------------------gtaagttcgtttattcg-tagtgtctatcttccttacgcgctctc-----gcagTTTATGCCGATGGAAGCATTTGTCTCGACATCCTCCAAAATCAGTGGAGCCCGATTTATGATGTTGCCGCAATACTGACATCGATCCAG

upper sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ16328 (Selaginella moellendorffii), 3'ss of exon 3

tcttaactatatgatggtactatcttctaatgcccacttatatgtgtcaccctgacatttttctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG
               |  | |  |||        |  | |  |   ||    |   | |  |||| |  |||||||||||||||||||| || ||| | || || ||||| ||||| ||||||||||| || ||||| || || || || ||||| || |||
---------------gtgagtcccttgcttctttctttgagtttcttctttttcttactcatctctt-cgcagTTTATGCTGATGGAAGTATTTGCCTCGACATTCTGCAAAATCAATGGAGTCCGATCTACGATGTTGCGGCAATTCTTACGTCCATACAG

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|211368006|gb|FL470437.1|FL470437

EST:     CCCCTGTGGGATGGAG                         ATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCA
genomic: CCCC-GTGGGATGGAGgttagtgaag ... atatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCA

EST: gi|211312738|gb|FL018802.1|FL018802

EST:     ACCTGATGATACCCCGTGGGATGGAG                         ATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCA
genomic: ACCTGATGATACCCCGTGGGATGGAGgttagtgaag ... atatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCA

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtcaccctgacatttttctcatatgcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG

                                tgctgat  putative branch site (score: 3)
         acattttt  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