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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaaccatagagtctatcttgttcgccccatttcttgtgttgagaatgcacaagagggccaatttgatttcgttcctcctgctactactactgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAGCAGCTGCAGAGGTACGGGGTCATCAGGTCGACCAAAGTCGCGGAGGTGA

Basic information

species Zea mays
transcript GRMZM2G423027_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423027_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g44280.2 (Oryza sativa), 3'ss of exon 1
gtcaaccatagagtctatcttgttcgccccatttcttgtgttgagaatgcacaagagggccaatttgatttcgttcctcctgctactactactgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAGCAGCTGCAGAGGTACGGGGTCATCAGGTCGACCAAAGTCGCGGAGGTGA
        |    || ||||  |  ||| ||| |||  |||||    |   |    ||   ||     |   ||| |||||| | ||  ||||| |||||||  | |||||||| |||||||| ||||||||||||||| | |||||||||||||| |||||||||||| | |||| ||||| ||| |||||| ||||||
aaggggattgatttcaatctcatatgcctcatctctcatgttgctgtttttctctgggaagaaccgtttcatgttgctcctggtgctgatactgttgcagCACCGACTGTGGTCAAGCGGGGCTAGCGACAAGAACAAGGCAATGGTTGAGCAGCTCCAGAGGTACGGGATTATCAAGTCGAGCAAGGTCGCGCAGGTGA
















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|211178416|gb|FL087632.1|FL087632
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211400276|gb|FL028896.1|FL028896
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211178414|gb|FL087630.1|FL087630
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|101382804|gb|EB813457.1|EB813457
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211178420|gb|FL087636.1|FL087636
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211402810|gb|FL028899.1|FL028899
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211402809|gb|FL028898.1|FL028898
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|71446834|gb|DR827884.1|DR827884
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211400277|gb|FL028897.1|FL028897
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|71442718|gb|DR823768.1|DR823768
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211178419|gb|FL087635.1|FL087635
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211322149|gb|FL087639.1|FL087639
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211178422|gb|FL087638.1|FL087638
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|71442719|gb|DR823769.1|DR823769
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211178421|gb|FL087637.1|FL087637
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211178417|gb|FL087633.1|FL087633
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211178415|gb|FL087631.1|FL087631
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
EST: gi|211402811|gb|FL028900.1|FL028900
EST:     AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAG                         CATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG
genomic: AAGAATCTAGGCGTCGTCTATCCAGCCCCGTCATCATCACCATGGAGGAGgtactccgct ... actgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcacaagagggccaatttgatttcgttcctcctgctactactactgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAGCAGCTGCAGAGGTACGGGGTCATCAGGTCGACCAAAGTCGCGGAGGTGA
                                            tactgat  putative branch site (score: 2)
                aatttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaaccatagagtctatcttgttcgccccatttcttgtgttgagaatgcacaagagggccaatttgatttcgttcctcctgctactactactgatgcagCATGGGCTGTGGTCCAGCGGGGCCAGCGACAAGAACAAGTCCATGGTTGAGCAGCTGCAGAGGTACGGGGTCATCAGGTCGACCAAAGTCGCGGAGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG