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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcactgcctggctctcatctctcctccatttacttgtcattgttgacattttagcagagtggcttgctacttgtgcagtacatgacatgtctatttactagtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG

Basic information

species Zea mays
transcript GRMZM2G008611_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 6
---------gtaagca-ctgcctggctctcatctctcctccatttact-tgtcattgttgacattttagcagagtggcttgctacttgt-gcagtacatgacatgtctatttactagtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG
           | | | |||  ||  | |  | | |||     | ||| ||  |     ||||||||| | ||  ||  |  |||  || |    | || |    | |  || ||     |  |   |   |||| |||||||||||| || |||||||| |||||||| |||||||||||||| |||||||||||||||||||| || ||||||
gtaagtgtttcacgtatctgtgtgtattttttttttccagttctcactctgctagctgcgacattttatcggaagggtattttaccagttgttcaagattatgcattttctttcttacccatatgtattttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGGTTTTGTTTCTTTCAGAAATCAGCAG

upper sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G17200.2 (Glycine max), 3'ss of exon 6
----------gtaagcactgcctggct------ctcatctctcctccatttacttgtc-attgttgacattttagcagagtggcttgctacttgtgca-gtacatgacat------gtctatttactagtttagcttggtaacttt-----------tgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG
           ||  | ||  ||   |      |||||  ||  |  ||||  | ||  | |   || |||||    ||   ||  | ||| ||      ||  ||| ||       | | | || ||   |    |||||| | |           | ||| ||||| || || |||||||| ||||| ||||| || ||||| |||||||| |||||||||||  |||| ||||||
gtaagtttttatataccctctctatttttccttctcattgctattttattttgtggtttacttcagatattttgttggaagtgca-gatacctgaatgtatatgtgaaatcaattcatatttgtagtatcatgatatggtaattatggtatgttggttacagTGATGCAAGGGTAATGTGGGATCAGAAGACAGGCCGTTCCAGGGGATTTGGATTTGTTTCTTTTCGGAATCAGCAG

upper sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 7
gtaagcactgcctggctctcatctctcctccatttacttgtcattgttgacattttagcagagtggcttgctacttgtgcagtacatgacatgtctatttactagtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG
              | ||  |  |  |  ||||     |  |  | |     |||| | ||  || |  || ||    ||| | |    ||   ||||| |||| ||| ||||| |     || ||| ||||| || || |||||||| ||||| ||||| || ||||| |||||||| |||||||||||  |||| ||||||
--------------gatcaaaattg-cggccatcctgctaccgctat-agtgttttgggaggctgacc-gccac----gcactgctatcca---ctattgactactttggcttgttgg---ttacagTGATGCAAGGGTAATGTGGGATCAGAAGACAGGCCGTTCCAGGGGATTTGGGTTTGTTTCTTTTCGGAATCAGCAG

upper sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 6
gtaagcactgcctggctctcatctctcctccatttac-ttgtcattgttgacattttagcagagtggcttgc-tacttgtgcagt--acatgacatgtctatttacta-gtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG
                               ||||    ||||     ||| | ||   | | |||   |    | |||||  |   || |  | || ||  | | |   |||    |||   ||    |||||||||||| ||||||||||| ||||| || || || || || |||||||| |||||||| ||| | || || |||
-----------------------------atatttgtactgtctcccatgatagttgtacggtgtgttctatacaattgtgttggtaacttagcttggctcatcattttattttttctggcggctc---cagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG

upper sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagcactgcctggctctcatctctcctccatttact-tgtcattgttgacattttagcagagtggcttgctacttgtgcagtacatgacatgtctatttactagtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG
                            |   |||  | |  |||  |   |||| | | |  |    | |    ||  |   | || || |  |||    || |       ||| ||   | || || ||||| || ||||||||||| |||||||| || || || ||||||||||| |||||||| ||| | ||||| |||
---------------------------gtaagttttttataccatcctcagcattcttgtattggaaatggaagtttaagatttgca-gaaac-tcttccgacaa-------ttgctattgtatgtagGGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGGATTTGTTTCCTTCCGTAACCAACAG

upper sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------------gtaagcactgcctggctctcatctctcctccatttacttgtcattgt---tgaca-------ttttagcagagtggcttgct-acttgtgcagtacatgacatgtctatttactagtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG
                                                   | | |   | ||   | || ||    |  |   |  | ||| | |   | |||        ||||        ||||  |   ||   ||||  || | |  ||| || | |   |     | ||   | ||  || || || || || ||||||||||||||||| ||||| || ||||| |||||||||||||| ||| | || ||||||
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcaga-atct-ttgatttaatatctatagTTCTTATTATAGGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG

upper sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 6
gtaagcactgcctggctctcatctctcctccatttacttgtcattgttgacattttagcagagtggcttgctacttgtgcagtacatgacatgtctatttactagtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG
|||||| | |  ||     |||  |   |   ||| ||| |     ||||  || |    || |  ||| |  |||||| |      |||   | |  |   |  | | |  |           |||||||||||| ||||||||||| |||||||| || || || || || ||||| |||||||||||| |||||||||||
gtaagctccgtttg-----catggcctttttgttttcttct-----ttgaatttgtgattgattaactttc--cttgtgtatgttgagactaatttgatccgtgttctggtat-----------cagAGATGCTAGGGTTATGTGGGATCAGAAAACTGGGCGTTCAAGGGGTTTTGGGTTTGTTTCTTTCCGGAACCAGCAG

upper sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 6
gtaagcactgcctggctctcatctctcctccatttacttgtcattgttgacattttagcagagtggcttgctacttgtgcagtacatgacatgtctatttactagtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG
                    || |   ||| | |   | | | || || |   || |    ||     |  |||||     ||     |       ||  |  |  |||  || ||     ||  |||||||| || ||||||||||| ||||| || || || || ||||| ||||| |||||||||||| | || || |||
------------------gaatgtggactc-actagttagaccttatt-atgattaaatgaagctatcttttactttcattgtcggaaa-------atagatgacattatgtttgtgctggttttagAGATGCGAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGAGGGTTTGGATTTGTTTCTTTCCGCAATCAACAG

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|161580653|gb|EY956343.1|EY956343
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGTGTTATGTGGGACCAAGAAAACAGGACGATCCA
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCA-GAAAACAGGACGATCCA
EST: gi|32927422|gb|CF032234.1|CF032234
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGTTC                         AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
EST: gi|32940921|gb|CF045740.1|CF045740
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGTGCTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
EST: gi|32927656|gb|CF032468.1|CF032468
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
EST: gi|32927013|gb|CF031825.1|CF031825
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
EST: gi|32850873|gb|CD990554.1|CD990554
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
EST: gi|6270004|gb|AW157975.1|AW157975
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC                         AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACG
EST: gi|32927394|gb|CF032206.1|CF032206
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
EST: gi|32928054|gb|CF032866.1|CF032866
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
EST: gi|32928740|gb|CF033552.1|CF033552
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
EST: gi|33092403|gb|CF052397.1|CF052397
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGCGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
EST: gi|32846545|gb|CD986226.1|CD986226
EST:     GTCACTGATGCTACTTTGTTCGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGTGCTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
EST: gi|166597480|gb|EG133910.1|EG133910
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGACTAGTGTTATGTGGGACCAGAAAACAGGACG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATG-CTAGTGTTATGTGGGACCAGAAAACAGGACG
EST: gi|166658931|gb|EG233793.1|EG233793
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACG
EST: gi|32928010|gb|CF032822.1|CF032822
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
EST: gi|32850928|gb|CD990609.1|CD990609
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC                         AGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgtgcagtacatgacatgtctatttactagtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG
                                        tggtaac  putative branch site (score: 2)
                                              cttttgc  CT-rich tract
                       tatttactagttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcactgcctggctctcatctctcctccatttacttgtcattgttgacattttagcagagtggcttgctacttgtgcagtacatgacatgtctatttactagtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT