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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacgcttggacgcttcgccatgatagtacatgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT

Basic information

species Zea mays
transcript GRMZM2G173534_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g70310.1 (Oryza sativa), 3'ss of exon 2
acacgcttggacgcttcgccatgatagtacatgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgct--gtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT
  | |       | |||   |||  |    |||| ||       |||  ||  | |    | | |    |||||| | || || |||||| ||  |||||||||||| || |||||||||||||| || |||||||||||  |||||||||||||||||||||| | |||||||||||||||||||||||| ||||| ||||
ttatgtcaaagtg-ttcttaatgccaac-tatgtctgactcgtttcatgttaatatctatagtttatcatctcattaccagttttcttctcctttgtgacagATGGACAGAGCTTCTATCCTTGGTGATGCAATTGAGTACTTGAAGGAGCTCCTGCAGAGGATTAACGATCTTCACAATGAACTTGAGTCTGCTCCTAGCT

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G38530.1 (Glycine max), 3'ss of exon 1
-acacgcttggac--gcttcgccatgatagtacatgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT-
  |||   |  |    | |    || |||  |    ||   |  |       || || | | |  | ||||    ||  |  | ||   ||    ||    ||||||| |||||||| |||||||| || ||||| |||||| ||||||| || ||||| |||||||| || |||||||||||| | |||||| | || |||  
ttcactaataaatcaacatatatatcatataatggcttcaatgctttaattgttactattggattttttgacatccaaaatgagtttgtttaaaatga---agATGGACAGGGCTTCAATCCTTGGGGATGCAATCGAGTATTTGAAGGAACTTCTGCAAAGGATCAGTGAGCTTCACAATGAATTGGAGTCAACACC-AGCAG

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G37750.1 (Glycine max), 3'ss of exon 4
acacgcttggacgcttcgccatgat-agtacatgtttggtattaatc--aacttgctttagtaaatg--ttgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT
      ||| || || |    | ||  ||    ||||||| |       ||  ||  |  ||   ||  ||   |  |||       | |  | || | ||| ||||||| |||||||| || ||||| || ||||||||||||||||||||||| ||||| |||||||  ||||| || || ||| | |||||  | |||    
-----gttgcacactactagttaattggtgttggtttggtttggggtggaatctggatctgtctctgggttctatgacattgtttggtttggtttggtttgatagATGGACAGGGCTTCAATTCTTGGGGATGCAATTGAGTATCTGAAGGAGCTTCTGCAAAGGATCAATGATCTGCATAACGAATTGGAGTCGACGCCGGTGG

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G05390.1 (Glycine max), 3'ss of exon 1
------acacgcttggacgcttcgccatga-tagtacatgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT-
         |  |||   | ||    | |  ||  |||  |    |||   |       ||| ||  |||| ||  | |  | |     | || |||| |     |||||||||||||||| || ||||| || |||||||| ||  |||||||| | |||||| |||| |  |||||||| || || || |||||| |||| | || 
ttgttgttgccattgactggtttattaaggctaagacacttcctttatgtgttggga-acttaag--aatggtg--tatggtaatgtcctttcatctgttt--gtagATGGATAGGGCTTCAATACTTGGGGATGCAATTGACTACTTGAAGGAGTTGCTGCAGCGGATTAATGATCTTCATAACGAGCTAGAGTCAACTCC-ACCTG

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G17330.1 (Glycine max), 3'ss of exon 3
acacgcttggacgcttcgccatga--tagtacatgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT
    | | | |    ||    | |  ||||    ||||||| |         | ||  |        ||  |   || |   | | |  | || | ||| ||||||| |||||||| || ||||| || ||||||||||||||||||||||| ||||| |||||||  ||||| || || ||  | || ||  | ||     
-ggggttagaatcaatcatagttaattagtgttggtttggtttgggctggaat-ctggatctgtctctggattctatgacattgtttggtttggtttgatagATGGACAGGGCTTCAATTCTTGGGGATGCAATTGAGTATCTGAAGGAGCTTCTGCAAAGGATCAATGATCTGCATAACGAGTTGGAATCGACACCAGTGG

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT3G26744.2 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------------------------------------acacgcttggacg--cttcgccatgatagtacat-gtttggtattaatcaacttgctttagtaaatgt----tgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT
                                                                             |   ||| | |  ||| |   |  |   || | |  ||   ||  |  |||   || || ||  |     ||||  |  |       | |    ||   |  ||||||||||| || || || ||||| || |||||||| ||||||||||| || || || |||||||  |||||||||||||||||||||||| ||||     
gtaaacacttactttgtctcttttatctccttaagagcttgtttacttgttgctgttatagagaattgttgtgttgtagctttgtagggcctttgttgttgtcaaactttgcatgtagttgctttactcttttgaggaagaggctcgtgatagtgttttatggattttcgatgaatttgcagATGGATAGAGCATCAATACTTGGAGATGCAATTGATTATCTGAAGGAACTTCTACAAAGGATCAATGATCTTCACAATGAACTTGAGTCAACTCCTCCTG

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv17s0000g00330.t01 (Vitis vinifera), 3'ss of exon 1
-acacgcttggacgcttcgccatgatagtac--atgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT
  |  | | | |  | |    | |||  |    | | |||  | |  |     ||| ||| | ||  | |  |   || ||  | | |   || || |||||||||||||||||||| |||||||| || |||||||||||  ||||||| || ||||| ||||||| | | || || |||||||| |||||  | ||     
tgctgggtggaatccattaataagatgtttttgaagcttgaaaattttagcagtgcctta-tgaaaatggcataatatgagt-tgtattggcttct-tgacagATGGATAGGGCTTCAATCCTTGGGGATGCAATTGAGTACTTGAAGGAACTTCTGCAAAGGATCAACAACCTCCATAATGAACTGGAGTCCACCCCTCCTG

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv14s0068g01200.t01 (Vitis vinifera), 3'ss of exon 1
------acacgcttggacgcttcgccatgatagtacatgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT-
         |  |||     |   | |||| |  |    |||||| ||  |  ||  | ||   | ||||| |  | | |   | | |  |  ||   | || ||||||||||| |||||||||||||| || || ||||||||  ||||||||||  |||| |||||||  ||||| || |||||||| || ||| | || | || 
atcagggatcagttgtggtttcttcaatgacacaattgctttggtgtt--tttacgcgttt--attaatgt-gtctattacttgaactaatgctcaaatttg-cagATGGATAGAGCTTCTATCCTTGGGGATGCCATTGAGTACTTGAAGGAGCTTTTGCAAAGGATCAATGATCTCCATAATGAACTGGAATCAACCCC-ATCTG

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0244g00130.t01 (Vitis vinifera), 3'ss of exon 1
acacgcttggacgcttcgcca--tgatagtacat-gtttggtat--taatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgctgt-gacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT
       |||||   ||      ||||| | ||| |||  ||    ||||    | | ||  | | || || |   | | | |  |   | ||||  ||| || |||||||||| ||||| ||||| |  || || ||||||||  |||||||| | ||||||||||||| ||| || || |||||||| |||||     |     
------atggaccgatcatagactgataatccattgttctgttgcataattggatggtttgggaagatatttaggattacctgtttaaatgttcttttgttgatagATGGATAGAGCTTCAATCCTGGCGGATGCTATTGAGTACTTGAAGGAGTTACTGCAGAGGATCAACGACCTCCAGAATGAACTGGAGTCTATCACACCTC

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S30_360V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------acacgcttggacgcttcgccatgatagtacatgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctct-tctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT
               ||| ||       ||   ||||    || ||  ||   |   |  |   |       |     | || |  ||  | ||  | |   | || ||  ||||||||| ||||| || || || ||||| ||||| ||||| || ||||||||||||||| | || |  ||  | ||||  || || ||  ||||        
gtttgtgaatatccccacactcaacaagttttacatg--cataaatacttcacacagaatacggtttaaggctttccatggagttgcagtaacacgtatgggtttggtg-aacagATGGACAGGGCCTCCATACTCGGCGATGCAATCGAGTACCTTAAGGAGCTCCTGCAGCGTATAAATGACATCCACAGCGAGCTCGATGCAGCGAAACAGG

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S257_22V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------acacgcttggacgcttcgccatgatagtacatgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT--
                        |     |  | |||     ||| | | |||  || |   |||  | | || ||    |||   |  | |  ||    ||       | ||     ||||||||| || || || || || || |||||||||||||| |||||||||||||| ||| | |||| |||  ||||||| || || ||   |||    || |  
gttcaacgcaccttcactctcgatcttatctatatgctgtatgatggttgcacacattagaggtta--cgattttct---ataaggttccagtgacacattcaaagtgggtatggc-caacagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCA--AAGTTGG

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S212_62V6.1 (Physcomitrella patens), 3'ss of exon 2
acacgcttggacgcttcgccatgatagtacatgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT--
                    ||| | | |||  || |   |||  | | || || ||     |   |   | | |    | ||   |   ||    ||||||||| || || || || || || |||||||||||||| |||||||||||||| ||| | |||| |||  ||||||| || || ||   |||    || |  
---------------gtatgatggttgcacacattagaggtta--cgattttctataa-ggttccagtgacactttcaaaattgggtatggcca--acagATGGACAGAGCCTCCATACTCGGTGACGCAATTGAGTACCTGAAGGAGCTCCTACAGCGCATCAACGACATTCACAACGAGCTGGAAGAAGCA--AAGTTGG

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ29742 (Selaginella moellendorffii), 3'ss of exon 1
-------------acacgcttggacgcttcgccatgatagtacatgtttggtattaatcaacttg---ctttagtaaatgttgattctcatcagcatttctcttctgctg----tgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT
             |  | || || |   | | |||       |  | |     ||      |||      ||  |      |   |||||    || |   |||    ||    || ||||||||||| || ||||| || || ||||| || |||||||| ||||||||||| |||||||||| ||| || ||||  || || ||     |  |     
gtgagtactttcaaaccactcgggcaacttggcattcactcgcccgctcctctttccatgcctttacctctttttctcctctcgctctcactcacactcaacttggtttgattttgtcagATGGATAGAGCATCTATTCTGGGTGACGCGATCGAGTATCTCAAGGAGCTCCTCCAGAGGATCAACGAGCTCCACAGCGAGCTGGAAGGCCCAGCAGATG

upper sequence: GRMZM2G173534_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ28242 (Selaginella moellendorffii), 3'ss of exon 1
-------------acacgcttggacgcttcgccatgatagtacatgtttggtattaatcaacttg----ctttagtaaatgttgatt---ctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT
             |  | || || |   | | |||       |  | |     ||      |||     ||||      | | | |    ||||    ||  |   ||    | || ||||||||||| || ||||| || || ||||| || |||||||| ||||||||||| |||||||||| ||| || ||||  || || ||     |  |     
gtgagtactttcaaaccactcgggcaacttggcattcactcgcccgctcctctttccatgcctttacctctttttctcctctcgctctcactcactctcaacttggtttgattttgtcagATGGATAGAGCGTCTATTCTGGGTGACGCGATCGAGTATCTCAAGGAGCTCCTCCAGAGGATCAACGAGCTCCACAGCGAGCTGGAAGGCCCAGCAGATG

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|29544520|gb|CB604900.1|CB604900
EST:     TCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAG                         ATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTC
genomic: TCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAGgtgatcaacc ... gctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTC
EST: gi|149084201|gb|EE173617.2|EE173617
EST:     TCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAG                         ATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTC
genomic: TCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAGgtgatcaacc ... gctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTC
EST: gi|149000812|gb|EE038037.2|EE038037
EST:     TCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAG                         ATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTC
genomic: TCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAGgtgatcaacc ... gctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTC
EST: gi|148965911|gb|EE016816.2|EE016816
EST:     TCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAG                         ATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTC
genomic: TCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAGgtgatcaacc ... gctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTC
EST: gi|149013527|gb|EE043014.2|EE043014
EST:     TCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAG                         ATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTC
genomic: TCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAGgtgatcaacc ... gctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTC
EST: gi|74241888|gb|DT649802.1|DT649802
EST:     TCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAG                         ATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTC
genomic: TCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAGgtgatcaacc ... gctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacttgctttagtaaatgttgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT
                 tgttgat  putative branch site (score: 4)
                                 catttctcttctgct  putative PPT
        tttagtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacgcttggacgcttcgccatgatagtacatgtttggtattaatcaacttgctttagtaaatgttgattctcatcagcatttctcttctgctgtgacagATGGATAGGGCTTCTATCCTTGGCGACGCAATTGAGTATCTGAAGGAGCTCCTGCAGAGGATCAGCGATCTTCACAATGAACTTGAGTCAGCTCCGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - -gccatga
- - - - - - - - - - - - - gtacatg
- - - - - - - - - - - - - - - - - - - - - aatcaac
- - - - - - - - - - - - - - - - - - - - - - - - -ttgcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat