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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_T01
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|32836609|gb|CD976287.1|CD976287
EST:     GTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG                         GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
genomic: GTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAG
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|32839843|gb|CD979524.1|CD979524
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

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), 47 (downstream exon)
Score: 398

GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 417

GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 340

GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 686

GCTACAATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTGgtataattac ... ttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccccattgtgatctacggaccgttgaccttatgcatgtgttgttttctttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA
                     cgttgac  putative branch site (score: 686)
                                        ttgttttcttt  putative PPT
                                           ttttcttt  TA-rich tract