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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcctaaagctattgtacctagaaaagccaaaacacaaaacagcctatagtttgggatggtgtatttactatgtatatcactgactgaaacttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGACATTGAGAAAGGGATAAACAACCTTGCAAAGAAGGCAAATGAGGGGGCGC

Basic information

species Zea mays
transcript GRMZM5G807639_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 11
-tatcctaaagc-tattgtacctagaaaagccaaaacacaaaacagcctatagtttggg-atggtgtatttactatgtatatcactgactgaaacttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGACATTGAGAAAGGGATAAACAACCTTGCAAAGAAGGCAAATGAGGGGGCGC
 || | | |  | || |   |||         ||  || | | || ||| |  || ||  ||     ||  |   |   | |||   ||   | |   |  |||| ||||||||||||||||||||||||||||||| |||||||||||| |||||||||||||||||||||  ||||||||||||||| | ||||||||| |
gtaacttgatacgtactagtcctgtgttg---aatccaaagatcatcctctgattgggttataagacatacatagtcactgtcatgtac-atatccattttagGGTCTTGTGGTGCCTGTTATCCGAGATGCTGATAACATGAACTTTGCGGACATTGAGAAAGGGATAAACGCCCTTGCAAAGAAGGCTACTGAGGGGGCAC

upper sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA14G02530.2 (Glycine max), 3'ss of exon 13
--------tatcctaaagctattgtacctagaaaagccaaaacacaaaacagcctatagtttgggatggtgtatttactatgtatatcactgactgaaacttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGACATTGAGAAAGGGATAAACAACCTTGCAAAGAAGGCAAATGAGGGGGCGC
        | | ||||   |   ||   | | |  ||||  | |   | || | |  |  |||   | |   |  || |      | |    |  |   |   ||||||||||||| || || ||||||||  ||||||||||||||||||||||||| || || ||   ||| ||     ||||||||||||||||||| ||  |  
tgtatatattttctaattttgcagttttttgcatggccatgaaaattatcaacatgcatgttgtatttgaacaaatattg-----accctcaatcg---ccattccagGGCCTTGTTGTACCGGTTATCCGCAATGCTGATACCATGAACTTTGCTGATATAGAAAAGCAGATTAATGCTTTTGCAAAGAAGGCAAATGATGGAACTT

upper sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA02G46200.1 (Glycine max), 3'ss of exon 13
tatcctaaagctattgtacctagaaaagcc--aaaacacaaaacagcctatagtttgggatggtgtatttactatgtatatc-actgactgaaacttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGACATTGAGAAAGGGATAAACAACCTTGCAAAGAAGGCAAATGAGGGGGCGC
 |   || || | |   |  ||| ||      | |   | |   |   |||      | ||| |||||||   |   ||||  ||   |     |   ||||||||||||| || || ||||||||  ||||||||||||||||||||||||| || || ||   ||| || |   ||||||||||||||||||| ||  |  
-agtatatag-tgtctaatttagcaattttttacatggctatgaaaattatcaacatgcatgttgtatttga-acaaatattgaccctcaattgccattccagGGCCTTGTTGTACCGGTTATCCGCAATGCTGATACCATGAACTTTGCTGATATAGAAAAGCAGATTAATACTTTTGCAAAGAAGGCAAATGATGGATCTT

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|93017174|gb|EB642694.1|EB642694
EST:     TCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCAGTGTTGCTGTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|32935625|gb|CF040437.1|CF040437
EST:     TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|211354774|gb|FL462364.1|FL462364
EST:     TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|16925492|gb|BM078560.1|BM078560
EST:     TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTGCATGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|211169877|gb|FL077606.1|FL077606
EST:     TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|60343714|gb|DN210687.1|DN210687
EST:     TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|6020821|gb|AW065749.1|AW065749
EST:     TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|6056485|gb|AW090875.1|AW090875
EST:     TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|16919656|gb|BM074297.1|BM074297
EST:     TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|6918383|gb|AW399913.1|AW399913
EST:     TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTGCCTGNTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|211104574|gb|FL031920.1|FL031920
EST:     GTTGGCACTTCCAAG                         GGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: GTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|7031253|gb|AW461141.1|AW461141
EST:     TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
EST: gi|60399105|gb|DN231919.1|DN231919
EST:     TACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAG                         GGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC
genomic: TACAGAGACTACGTAGACGTCAGTGTTGCTGTTGGCACTTCCAAGgtgccatatt ... acttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatagtttgggatggtgtatttactatgtatatcactgactgaaacttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGACATTGAGAAAGGGATAAACAACCTTGCAAAGAAGGCAAATGAGGGGGCGC
                                  cactgac  putative branch site (score: 2)
                                              cttctcc  putative PPT
                  tatttactatgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcctaaagctattgtacctagaaaagccaaaacacaaaacagcctatagtttgggatggtgtatttactatgtatatcactgactgaaacttctccagGGCCTTGTGGTGCCTGTTATCCGAGATGCTGATACCATGAACTTTGCTGACATTGAGAAAGGGATAAACAACCTTGCAAAGAAGGCAAATGAGGGGGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG