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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataattactactactgcatccgttagcctgtatggccccattgtgatctacggaccgttgaccttatgcatgtgttgttttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA

Basic information

species Zea mays
transcript GRMZM2G075719_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
gtataattac---tactactgca--tccgttagcctgtatggccccattgtgatctacggaccgttgaccttatgca---tgtgttgttttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA
|||| ||  |   |  | |||||  |||  |    |||    | || | |  |||  | | |  |  | ||||||||   ||| || |||| | |||||||||||||||||||||||| | ||||||||||| |||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||
gtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcatt--atcttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G16200.1 (Glycine max), 3'ss of exon 2
------------gtataattactactactgcatccgttagcctgtatggccccattgtgatctacggaccgttgaccttatgcatgtgttgttttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA
            ||    ||  || |  |   |   ||    | | |       || |      |  | | || || || |   | | ||  ||| |   ||||||||||||||| |||||||| || || ||| | ||||||||||| || || ||||| || |||||||||||||| |  ||||||||||
aagcagtacactgttggctttttatttttatttttattgaattctcttaatt--ttcttcctctcaaaacctttactttttatttttcttcatttgtg-acagGGATACAGCTGGCCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G04330.1 (Glycine max), 3'ss of exon 2
---------gtataattactactactgcatccgttagcctgtatggccccattgtgatctacggaccgttgaccttatgcatgtgttgttttctttg-cagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA
         ||  ||||| |   ||  | ||  ||  |  ||   |     || |  ||| | |   |||     | | ||| | ||  | | || | ||||||||||||||| |||||||| || || ||| | ||||||||||| || || ||||| || || ||||| |||||||  ||||||||||
tgggttttagttcaattaatgacacaccttcttttgactggtggagttttttttttttctcccggt-gttcctaatgttcatcttttcatgttttcgacagGGATACAGCTGGCCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTAGCTGTTATTGTATATGATGTTGCAA

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 2
------------------gtataattactactactgcatccgttagcctgtatggccccattgtgatctacggaccgttgaccttatgcatgtgttgttttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA
                  ||  ||||| |   ||  | |   ||  |  ||   |     || |   |  |  |   || | ||| | |||||||| |        ||||||||||||||| |||||||| || || ||| | ||||||||||| ||||| ||||| || || ||||| |||||||  ||||||||||
gtgcatcgttgggttttggttcaattaatgacacccctttatttgactggtggagttttttttt--cccccctaatattcatctttt-catgtgttatg------acagGGATACAGCTGGGCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATCAGGGACTCATCTGTAGCTGTTATTGTATATGATGTTGCAA

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G05860.1 (Glycine max), 3'ss of exon 2
-------gtataattactactactgcatccgttagcctgtatggccccattgtgatcta---cggaccgttgaccttatgcatgtgttgttttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA
       ||| |  ||   ||  |   |   ||    || ||   |  | | |  |  |   |    | || || ||     | | ||   ||  |  ||||||||||||||| |||||||| || || ||| | ||||||||||| || || ||||| || |||||||||||||| |  ||||||||||
ataagcagtaca-ctatagctttttttttttttttattgaattctcttagttttcttcatctcaacaccttcacttttaatttttttttcatttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
gtataattacta--ctactgcatccgttagc--ctgtatggccccattgtgatctacggaccgttgaccttatgcatgtgttgttttcttt--gcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA
|||  ||    |  ||  | ||    |      ||| |      |||||      |      | |||       |  | |  |   || |    ||||||||||||||| || ||  | ||||||||| ||||||| ||||||||||| || || || |||||||| ||||| |  ||||||||||
gtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 2
-----gtataattactactac-tgcatccgttagcctgtatggccccattgtg-atctacggaccgttgaccttatgcatgtgttgttttcttt---gcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA
     || | |||    |||  |||| |  ||      ||||   | |  | | || |    |   ||   |||   ||| |  | ||| || |   | ||||||||||| || |||||||| ||||||||| | ||||| ||||| || || || || || ||||| ||||||||||  ||||||||||
gatgagtgtgattgagcctagatgca-caatttattcctatgctactaacgagcatgttgtcattatttctctttgacatttcatttttgctcttatgtagGGATACAGCCGGGCAGGAAAGATTCAGGAGTCTCATTCCGAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAA

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 2
-gtataattactactactgcatccgttagcctgtatggcccca--ttgtgatctacggaccgttgaccttatgcatgtgttgttttct-------ttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA
  |||  ||  ||| |   |||   ||      |     || |   | | ||||   ||  | | |   | ||  | | || |||| |       || ||||||||| || || |||||||||||||||||| | || ||||| || || || ||||| || ||||| ||||||||||  ||||||||||
aatatttttg-tacaatctcatgttttgaaacatcaaatccaagtctataatctgacgatggctaattgtctgtttcttttcttttttctttttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAA

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 3'ss of exon 3
gtataattactactactgcatccgttagcctgtatggccccattgtgatcta----cggaccgttgaccttatgc--atgtgttgttttctt----tgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA
   ||  ||     |  |     ||   | ||| |     | |  || | ||    || |    |||    ||    || ||  | | |  |    ||||||||||| ||||| ||||| |||||||||||||||||||| || || ||  | || || || || || ||  |||| | ||||||| |||
-attagataacgagatggaggttgtcttcttgtttcttgacgtcttgttgtagaaacgaaatactgaatccatcataatttggggctgttatgaaatgcagGGATACCGCTGGACAGGAGAGGTTCAGGAGTTTAATTCCTAGTTACATTCGGGATTCGTCCGTGGCAGTGGTTGTGTACGATGTTTCAA

upper sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S456_9V6.1 (Physcomitrella patens), 3'ss of exon 3
--------gtataattactactactgcatccgttagcctgtatggccccattgtgat--ctacggaccgttgaccttatgcatgtgttgttttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA
         | | || |    ||     |  |  |      || |||   | |  ||  | |  ||   |   |   |     |  |  | |    || ||||| |||||||| || || |||||||||||||||||||| ||||| ||  ||||||| || || || ||  |||| | ||||||| | |
agtactccttgtgataatggttatcttttttgc-acatgacattgccttgtggaaattcccattgaatttcatcagaaaatgggactgttatgaaatgtagGGACACAGCTGGACAAGAGAGGTTCAGGAGTTTAATTCCCAGCTACATTCGAGACTCGTCTGTGGCAGTAGTTGTTTACGATGTTTCGA

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|211109341|gb|FL282964.1|FL282964
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
EST: gi|32840351|gb|CD980032.1|CD980032
EST:     TACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
genomic: TACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
EST: gi|211109340|gb|FL282963.1|FL282963
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACT-CAACTCTG                         GGATACAGCTGGTCGGGAAAKGGTTCAGGAGTTTAATTCCAAGCTATATCA
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAA-GGTTCAGGAGTTTAATTCCAAGCTATATCA
EST: gi|116822600|gb|EC866010.1|EC866010
EST:     CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
genomic: CTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
EST: gi|32836609|gb|CD976287.1|CD976287
EST:     GTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
genomic: GTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccccattgtgatctacggaccgttgaccttatgcatgtgttgttttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA
                     cgttgac  putative branch site (score: 4)
                                        ttgttttcttt  putative PPT
                                           ttttcttt  TA-rich tract