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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcactgcctggctctcatctctcctccatttacttgtcattgttgacattttagcagagtggcttgctacttgtgcagtacatgacatgtctatttaccagtttagcttggtaacttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG

Basic information

species Zea mays
transcript GRMZM5G835213_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 6
---------gtaagca-ctgcctggctctcatctctcctccatttact-tgtcattgttgacattttagcagagtggcttgctacttgt-gcagtacatgacatgtctatttaccagtttagcttggtaacttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG
           | | | |||  ||  | |  | | |||     | ||| ||  |     ||||||||| | ||  ||  |  |||  || |    | || |    | |  || |      |  |   |   |||| ||||||||||||||| |||||||| |||||||| |||||||||||||| |||||||||||||||||||| || ||||||
gtaagtgtttcacgtatctgtgtgtattttttttttccagttctcactctgctagctgcgacattttatcggaagggtattttaccagttgttcaagattatgcattttctttcttacccatatgtattttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGGTTTTGTTTCTTTCAGAAATCAGCAG

upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G17200.2 (Glycine max), 3'ss of exon 6
----------gtaagcactgcctggct------ctcatctctcctccatttacttgtc-attgttgacattttagcagagtggcttgctacttgtgca-gtacatgacat------gtctatttaccagtttagcttggtaacttt-----------tgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG
           ||  | ||  ||   |      |||||  ||  |  ||||  | ||  | |   || |||||    ||   ||  | ||| ||      ||  ||| ||       | | | ||  |   |    |||||| | |           | ||| ||||| ||||| |||||||| ||||| ||||| || ||||| || ||||| |||||||||||  |||| ||||||
gtaagtttttatataccctctctatttttccttctcattgctattttattttgtggtttacttcagatattttgttggaagtgca-gatacctgaatgtatatgtgaaatcaattcatatttgtagtatcatgatatggtaattatggtatgttggttacagTGATGCAAGGGTAATGTGGGATCAGAAGACAGGCCGTTCCAGGGGATTTGGATTTGTTTCTTTTCGGAATCAGCAG

upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 7
gtaagcactgcctggctctcatctctcctccatttacttgtcattgttgacattttagcagagtggcttgctacttgtgcagtacatgacatgtctatttaccagtttagcttggtaacttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG
              | ||  |  |  |  ||||     |  |  | |     |||| | ||  || |  || ||    ||| | |    ||   ||||| || | ||| ||||| |     || ||| ||||| ||||| |||||||| ||||| ||||| || ||||| || ||||| |||||||||||  |||| ||||||
--------------gatcaaaattg-cggccatcctgctaccgctat-agtgttttgggaggctgacc-gccac----gcactgctatcca---ctattgactactttggcttgttgg---ttacagTGATGCAAGGGTAATGTGGGATCAGAAGACAGGCCGTTCCAGGGGATTTGGGTTTGTTTCTTTTCGGAATCAGCAG

upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 6
gtaagcactgcctggctctcatctctcctccatttac-ttgtcattgttgacattttagcagagtggcttgc-tacttgtgcagtacatgacatgtctatttaccagtttagcttgg-taacttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG
                               ||||    ||||     ||| | ||   | | |||   |    | |||||  |   |    |  |    | | || ||||  ||   |  |   | |||||||||||||||||||||||| ||||| || || || || || || ||||| |||||||| ||| | || || |||
-----------------------------atatttgtactgtctcccatgatagttgtacggtgtgttctatacaattgtgttg-gtaacttagcttggctcatcattttattttttctggcggctccagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG

upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------------gtaagcactgcctggctctcatctctcctccatttacttgtcattgt---tgaca-------ttttagcagagtggcttgct-acttgtgcagtacatgacatgtctatttaccagtttagcttggtaacttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG
                                                   | | |   | ||   | || ||    |  |   |  | ||| | |   | |||        ||||        ||||  |   ||   ||||  || | |  ||| || |     |     | ||   | ||  || || || || || ||||||||||||||||| ||||| || ||||| |||||||||||||| ||| | || ||||||
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcaga-atct-ttgatttaatatctatagTTCTTATTATAGGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG

upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 6
gtaagcactgcctggctctcatctctcctccatttacttgtcattgttgacattttagcagagtggcttgctacttgtgcagtacatgacatgtctatttaccagtttagcttggtaacttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG
|||||| | |  ||     |||  |   |   ||| ||| |     ||||  || |    || |  ||| |  |||||| |      |||   | |    | | || |    ||||| |      ||||||||||||||||||||||| |||||||| || || || || || ||||| |||||||||||| |||||||||||
gtaagctccgtttg-----catggcctttttgttttcttct-----ttgaatttgtgattgattaactttc--cttgtgtatgttgagactaatttg---atccgtgt--tctggtatc------agAGATGCTAGGGTTATGTGGGATCAGAAAACTGGGCGTTCAAGGGGTTTTGGGTTTGTTTCTTTCCGGAACCAGCAG

upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 6
gtaagcactgcctggctctcatctctcctccatttacttgtcattgttgacattttagcagagtggcttgctacttgtgcagtacatgacatgtctatttaccagtttagcttggtaacttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG
                    || |   ||| | |   | | | || || |   || |    ||     |  |||||     ||     |       ||  |  |  |||  || ||     ||  |||||||| |||||||||||||| ||||| || || || || ||||||||||| |||||||||||| | || || |||
------------------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|24934275|gb|CA452493.1|CA452493
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC                         AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
EST: gi|71436375|gb|DR817425.1|DR817425
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC                         AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
EST: gi|71324258|gb|DR798829.1|DR798829
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC                         AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
EST: gi|31361403|gb|CD445760.1|CD445760
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC                         AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
EST: gi|22546594|gb|BU098905.1|BU098905
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC                         AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
EST: gi|22545671|gb|BU098030.1|BU098030
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC                         AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
EST: gi|29544652|gb|CB605032.1|CB605032
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC                         AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
EST: gi|71317247|gb|DR795307.1|DR795307
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC                         AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
EST: gi|194717059|gb|FK934212.1|FK934212
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC                         AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
EST: gi|5268356|gb|AI770320.1|AI770320
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC                         AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
EST: gi|32866442|gb|CF006124.1|CF006124
EST:     GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC                         AGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG
genomic: GTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 709

GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 371

GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 420

GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 988

GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactg ... acttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgtgcagtacatgacatgtctatttaccagtttagcttggtaacttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG
                                        tggtaac  putative branch site (score: 988)
                                              cttttgc  CT-rich tract
                     tctattta  TA-rich tract