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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 3
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaaca--atgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT
                                                                 |||    | | ||||||    ||   ||    |||||   || |||    |     |    ||  |  ||  ||| | ||||  ||| |||  | |||| ||||||||| ||||||||| |||| || || || |||||||| |||||| | |||||||||||||||||||||||||||||||| ||||||||||||||||| ||
-----------------------------------------------------------------atgatttttaatagcaatgtcatttttaattcgttttgcattataaaagctctttcct---atcctgcctcctttttccttaaatttgttt--tacatgctgtagGCAGACAGTCTTTCCTAAACACTTCAAAATGGATAGAGGAAGTTAGAACTGAGAGGGGCAGTGATGTTATCATTGTGCTGGTTGGGAACAAAACTGATCT

upper sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G04340.1 (Glycine max), 3'ss of exon 4
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttt-tatcttttaaggattaaggacataaatttttactattttattcttacc-tttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT
                                                                       |||  |||  ||  |  || |||  | | ||  |  |    ||       | || | |||     ||  |||| ||   | |||| | | |||   ||||| | ||  ||||| |||| ||||| | |||||| || || || |||| |||||| |||||||||| ||| ||||| | |||||||||||||||||||||
--------------------------------------------------------------------attatccatagtcacctt--cttggatctctgtacatgatttcaatagtcactagaagtctttgaaggttgcttctaactactcatttttcttatgaaatagGCCGTCAAACTTTCCTAAACACATCAAGGTGGATTGAAGAGGTGCGCATTGAGAGAGGCAGTGATGCTATTATTGTTCATGTTGGGAACAAAACTGACCT

upper sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 3
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT
                                                         | ||||   |  |||| | | | || ||||  | || |    | ||| ||| |   |  |   | |||   |||  ||         |  |||  |  |||  |  | ||||| ||||| |||||||||||||  | |||||||| || || || || || || || ||||||||||| || ||||| |||||||||||||||||||| ||
---------------------------------------------------------gttatctc-tctacatgatttg-aataatgtgttggcataagtgtctgttacgagctctgtcaagaaaacattatgat---------aaatttgatatttttgttgtatagGCCGGCAGACTTTCTTAAATACTGCTAAGTGGATTGAAGAGGTGCGAACAGAAAGAGGCAGTGATGTCATTATTGTTCTTGTTGGGAACAAAACTGATCT

upper sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G05860.1 (Glycine max), 3'ss of exon 3
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacc-tttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT
                                                                    | |   ||  | |   ||  |      |  |  | ||||    | |      | | | ||| |        |||| |   || |    | | | | | ||||| | ||| ||||| |||| ||||| |||||||| || || || |||| ||| || ||||| ||||||||  | || |||||||||||||||||||| ||
--------------------------------------------------------------------ctctctagatg-attcatatcacatgtgcatagttttttgttcactgttcctaaacactttgatggacactttctgattattcagccttcttacgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAAAGAGGCAGCGATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCT

upper sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G04330.1 (Glycine max), 3'ss of exon 3
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT
                                                                    ||||| | | | || ||| | | || |    | ||| | |||  | |||  | |   |    |  | ||| |  | |  || || | |||  |  | ||||| ||||| ||||| |||||||  | |||||||| || || || || || ||||| ||||||||||| || ||||| |||||||||||||||||||| ||
-----------------------------------------------------------------tctcacatgatttg-aataataagttggcataagtgtctgtcaagactcaagagc-tctgtcaagaaaactttctgataaatttgatat-ttttgttgtatagGCCGGCAGACTTTCCTAAATACTGCAAAGTGGATTGAAGAGGTGCGAACAGAGAGAGGCAGTGATGTCATTATTGTTCTTGTTGGGAACAAAACTGATCT

upper sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G41090.1 (Glycine max), 3'ss of exon 4
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT
                                                                |||   ||  |||  |  | |    |  |   ||  || ||||  | |||    | | | | ||| |   ||   |        | |||| | | |||   ||||| | ||  ||||| | || ||||| |||||||| || || || |||| |||||| |||||||||||||| ||||| |||||||||||||||||||||||
----------------------------------------------------------------gat-tgcaatagt--ctgccaactgtccgtgcttaaattttttgggcattttctaga-agactttgaaggttgcttctaattactcatttttcttatgaaatagGCCGCCAAACTTTCCTGAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAGAGAGGCAGTGATGTTATTATTGTTCTTGTTGGGAACAAAACTGACCT

upper sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G16200.1 (Glycine max), 3'ss of exon 3
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT
                                                                ||  || |||| |     ||  |  |         | |   | |||   |||  || |  ||    | | | | ||| ||      |    | |  || | ||||| | ||| ||||| |||| ||||| |||||||| || || || |||| ||| || ||||| ||||||||  |||| |||||||||||||||||||| ||
--------------------------------------------------------------ttgactcatatca-tgtgtgcatagttttttgttcactgttcctaaagtcctaaacactttgatggacagtttctgattgtt-----cagcattcttgtgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTGAAAGAGGCAGCGATGTTATTGTTGTTCTTGTTGGGAACAAAACTGATCT

upper sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 3
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT
                                                     | ||| | |  ||   |  |  | |    |||  ||||     |||| | | |   | ||    ||  | | ||||||      || |||  |   | |||||     ||| ||||||||||||| ||| | || ||  |||||||||| || || ||||| |||||| | |||||||||||||||||||| ||||||||||||||||| |||||
-----------------------------------------------------acatg-ttttggactaattttggcattggcaa--acta---ttttttgtatatgttgcatctgtgatgtgattttttaac----tactctggcacctttttgt-----gttttagGCAGGCAGTCATTCCTTAACACTGCCAAGTGGATTGAGGAGGTTCGTACTGAGCGAGGCAGTGATGTTATCATTGTCCTTGTTGGGAACAAAACAGACCT

upper sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 3
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaagg-acataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT
                                                                  |    || |  | |       |||      ||| ||  ||| |  |||  |  ||    |    |   ||||| |  ||    |||||   ||  || |  |||  |||| |||||| |||| || || |||||||| || || |||||||||||||| || ||||||||||| || || |||||||| ||||| ||||||||
------------------------------------------------------------------tctttatgaa-aacgttttgaactttcttatttaattgtttcattattgtgttaccattaccgatgaaattttctgattggacttattatctt--tgattaagGTCGGCAATCTTTCCTAAACACTTCAAAGTGGATTGAAGAGGTTCGCACTGAGAGAGGTAGTGATGTTATTATCGTCCTTGTTGGAAACAAGACTGACCT

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:     AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
genomic: AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
EST: gi|32840351|gb|CD980032.1|CD980032
EST:     AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
genomic: AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
EST: gi|211109340|gb|FL282963.1|FL282963
EST:     AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
genomic: AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
EST: gi|116822600|gb|EC866010.1|EC866010
EST:     AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
genomic: AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
EST: gi|32836609|gb|CD976287.1|CD976287
EST:     AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
genomic: AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaggacataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT
                          ttcttac  putative branch site (score: 2)
                                cctttatttgtttc  CT-rich tract
       ataaatttttactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG