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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTATGTGGTCTTTATGCTGTCAGCCTGTGCTCTCTTCTCAAAGACATGGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccatgtacatgccactcaaaactagtatcatcaaagcacatgccgttgtgcttgtccgtgcctattttacttctttatgaattcaaatttgcca...

Basic information

species Zea mays
transcript GRMZM2G307252_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G307252_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 5'ss of exon 5
GTTCTATGTGGTCTTTATGCTGTCAGCCTGTGCTCTCTTCTCAAAGACATGGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccatgtacatgccactcaaaactagt-atcatcaaagcacatgccgttgtgcttgtccgtgcctattttacttctttatgaattcaaatttgcca-
||||||||||||||| ||||||||||| |||||||||||||||||||||||||||||||| ||||| ||||| || ||||| |||||||| ||||||||||||||    |  | |      |   | ||||| ||  |    |   |  |  | || |   ||  | | |    |   |  | |||  || || | ||  | 
GTTCTATGTGGTCTTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCTGGCTCATCTGCAAAGGATGTTGCTAAACAGCTGAAGgtaaagatgtagatacatattttctatctagttattgttcctgtttac-ctatagtccaactcattacattgcatgtgtggtgatgtctt-aagtctgatat

upper sequence: GRMZM2G307252_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 5'ss of exon 5
GTTCTATGTGGTCTTTATGCTGTCAGCCTGTGCTCTCTTCTCAAAGACATGGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccatgtacatgccactcaaaactagt-atcatcaaagcacatgccgttgtgcttgtccgtgcctattttacttctttatgaattcaaatttgcca-
|||||||||||| || ||||||||||| |||||||||||||||||||||||||||||||| ||||| ||||| || ||||| |||||||| ||| ||||||||||    |  | |      |   | ||||| ||  |    |   |  |  | || |   ||    | | |  |   |  | |||  || |  | ||  | 
GTTCTATGTGGTATTCATGCTGTCAGCTTGTGCTCTCTTCTCAAAGACATGGATTGAAGTATCTGGCTCATCTGCAAAGGATGTTGCTAAACAGTTGAAGgtaaagatgtagatacatattttctatctagttattgttcctgtttac-ctatagtccagctcataacatttcgtgtgtggtgatgtctt-atgtatgatat

upper sequence: GRMZM2G307252_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA12G35990.1 (Glycine max), 5'ss of exon 6
GTTCTATGTGGTCTTTATGCTGTCAGCCTGTGCTCTCTTCTCAAAGACATGGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccatgtacatgccactcaaaactagtatcatcaaagcacatgccgttgtgcttgtccgtgcctattttacttctttatgaattcaaatttgcca
||||||| | || |||||||| ||||| |||||  | |||||||| |||||||||||||| ||||||||||| || |  || ||||| |||||||||||||||  | |  | |         || | |   |  |     |  | ||     |    |    |      || |||  |     ||  ||  |     |  
GTTCTATCTTGTGTTTATGCTTTCAGCTTGTGCCTTGTTCTCAAAAACATGGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCCAAGCAGCTGAAGgtacgaactggcattcattttgcataccatttccctattgacgatatatttcttaagtaaagcagcagaatattagctaggcttgggttttagccatctt

upper sequence: GRMZM2G307252_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA12G17950.1 (Glycine max), 5'ss of exon 6
GTTCTATGTGGTCTTTATGCTGTCAGCCTGTGCTCTCTTCTCAAAGACATGGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccatgtacatgccactcaaaactagtatcatcaaagcacatgccgttgtgcttgtccgtgcctattttacttctttatga--attcaaatttgcca---
 |||||  | || |||||| |||||||||||||  | ||||| || || ||||||||||| ||||||||||| || |  || ||||| |||||||| ||||||  ||    | || ||   |    |    ||| ||  |      |   ||| ||  | || |   || |  ||||| | |||    |  |   |||  ||   
ATTCTACCTTGTGTTTATGTTGTCAGCCTGTGCCTTGTTCTCTAAAACTTGGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTCAAGgtattactgact-cacgcattttgggaaatttattattta--ttatttttgttttg--tatctgcaactttagtacttatatatagcgagcctgttttcacatca

upper sequence: GRMZM2G307252_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA13G34370.1 (Glycine max), 5'ss of exon 6
GTTCTATGTGGTCTTTATGCTGTCAGCCTGTGCTCTCTTCTCAAAGACATGGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccatgtacatgccactcaaaactagtatcatcaaagcacatgccgttgtgcttgtccgtgcctattttacttctttatgaattcaaatttgcca--
||||||| | || |||||||| |||||||||||  | ||||| || |||||||||||||| ||||||||||| || || || ||||| |||||||| ||||||    |  | |  ||    |  | |||  | ||  ||  | |||||   |  | |||        |      |    | |  |  ||    |||   |  
GTTCTATCTTGTGTTTATGCTTTCAGCCTGTGCCTTGTTCTCTAAAACATGGATTGAAGTCTCTGGTTCATCTGCTAAAGATGTTGCCAAGCAGCTTAAGgtactgactagcat-tgattttgtatactcttttccccattg-acatgatatatttcttaagtaaagcagcaaaataattgttaggctttgggttttagagc

upper sequence: GRMZM2G307252_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA06G32680.1 (Glycine max), 5'ss of exon 6
GTTCTATGTGGTCTTTATGCTGTCAGCCTGTGCTCTCTTCTCAAAGACATGGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaa-aaccatgtacatgccactc---aaaactagtatcat-caaagcacatgccgttgtgcttgtccgtgcctattttacttct-ttatgaattcaaatttgcca
 |||||  | || |||||| |||||||||||||  | ||||| || || ||||||||||| ||||||||||| || |  || ||||| |||||||||||||||   || ||  ||||||   |     ||  || |||  |     | |  ||         | |  | |   |||  |    || || |    ||| |||     
ATTCTACCTTGTGTTTATGTTGTCAGCCTGTGCCTTGTTCTCTAAAACTTGGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgactata-acatgcatttttgtgaatttactattttgttttgtatctggaagaacattagcacttcaatataatgagcctgttttctcatcatatt-----

upper sequence: GRMZM2G307252_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA06G32680.2 (Glycine max), 5'ss of exon 6
GTTCTATGTGGTCTTTATGCTGTCAGCCTGTGCTCTCTTCTCAAAGACATGGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaa-aaccatgtacatgccactc---aaaactagtatcat-caaagcacatgccgttgtgcttgtccgtgcctattttacttct-ttatgaattcaaatttgcca
                          |||||||  | ||||| || || ||||||||||| ||||||||||| || |  || ||||| |||||||||||||||   || ||  ||||||   |     ||  || |||  |     | |  ||         | |  | |   |||  |    || || |    ||| |||     
--------------------------CCTGTGCCTTGTTCTCTAAAACTTGGATTGAAGTCTCTGGTTCATCTGCTAGAGATGTTGCAAAGCAGCTGAAGgtactgactata-acatgcatttttgtgaatttactattttgttttgtatctggaagaacattagcacttcaatataatgagcctgttttctcatcatatt-----

upper sequence: GRMZM2G307252_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 3
GTTCTATGTGGTCTTTATGCTGTCAGCCTGTGCTCTCTTCTCAAAGACATGGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccatgtacatgccactcaaaact-agtatcatcaaagca--catgccgttgtgcttgt-ccgtgcctattttacttctttatgaattcaaatttgcca
 |||||| |  |||||||| || | |||||||| || ||||||||||| ||||||||||| ||||| || || || |  || || ||||||||||| ||||||  |     |     | |  |    || | | |  |||   |   | | |  |||||||  |   |     |   |  |  |||  |     |   |     
CTTCTATCTAATCTTTATGTTGGCTGCCTGTGCACTTTTCTCAAAGACTTGGATTGAAGTATCTGGATCCTCTGCTAGAGATGTGGCTAAGCAGCTCAAGgtatgaattctttgggactatacttgtcttaattttgtcatccccttcctacttttgtgctgttattgaaatgagggttttgttttgggggccaaggatc----

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|5525475|gb|AI861368.1|AI861368
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|40302792|gb|CK347179.1|CK347179
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|32846329|gb|CD986010.1|CD986010
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|211438473|gb|FL466383.1|FL466383
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|5525766|gb|AI861659.1|AI861659
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|211435890|gb|FL466382.1|FL466382
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|71426282|gb|DR807332.1|DR807332
EST:     TTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: TTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|37388526|gb|CF631472.1|CF631472
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATTGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|78024965|gb|DV493352.1|DV493352
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|6695437|gb|AW288545.1|AW288545
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|211223105|gb|FL468693.1|FL468693
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCCGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|211221054|gb|FL468692.1|FL468692
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAASCAGCTGAAG                         GAGCAACAAATGGTGATGCCCGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|45567388|gb|CK985547.1|CK985547
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|67024545|gb|CO453294.1|CO453294
EST:     GCGAAGGACTGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GCGAAGGAC-GTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|71305340|gb|DR788803.1|DR788803
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|78025522|gb|DV493909.1|DV493909
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
EST: gi|5915599|gb|AW053240.1|AW053240
EST:     GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAG                         GAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA
genomic: GGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccat ... aattcaacagGAGCAACAAATGGTGATGCCAGGCCATCGTGAGTCAAACCTGCAAAGGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTATGTGGTCTTTATGCTGTCAGCCTGTGCTCTCTTCTCAAAGACATGGATTGAAGTTTCTGGTTCATCAGCGAAGGACGTTGCTAAGCAGCTGAAGgtaaaaccatgtacatgccactcaaaactagtatcatcaaagcacatgccgttgtgcttgtccgtgcctattttacttctttatgaattcaaatttgcca

- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG