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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgggcggtgtatatatttttgttttatatcgttgtttggatcttgatctggccggctgatgaatacgtgcttctctctccgacgaacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGGAGGAGTCCATCGTGGCCGACGGCAACGGCAAGGAGGAAGAGGTCGGGGT

Basic information

species Zea mays
transcript GRMZM2G127949_T07
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127949_T07 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g63770.1 (Oryza sativa), 3'ss of exon 1
-------------------------------gtacgggcggtgtatatatttttgttttatatcgttgtttggatcttgatctggccggctgatgaatac-gtgct--------tctctctccgacgaacg-----acgca-----gCGGGCGGAGACGGGAA--GGCCGTGCGCTCA--AGGATGGCGCGCGAGCAGCTGGAGGAGTCCATCGTGGCCGACGGCAACGGCAAGGAGGAAGAGGTCGGGGT
                                | | |  ||||  | |  |||| |||  |  ||  ||  |  || || ||||    | | |   |||  |||||        |||   |||||||  ||     |||||     || |  |  |||||| |  ||| | | | |||  | | || |||||||||||  ||||||| |||||||||| ||| |||||||||||||||| |||||||||| 
gttggtgctcttcttcttcttcttcttgctgctgcagctggtg-gtgttgttttttttattggcggggtcggtttcctgctctgttttgttaagtcatattgtgctgtcctggatcttgatccgacgtccgtccgtacgcactcacgcagCTGACGACGGGGAAGGGCGGCGTGGTCAGCATGGTGCCGCGCGAGCAGGCGGAGGAGGCCATCGTGGCTGACAGCAACGGCAAGGAGGAGGAGGTCGGGG-
















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|89247965|gb|DY619751.1|DY619751
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|148978794|gb|EE026318.2|EE026318
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|88755867|gb|DY540008.1|DY540008
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|71773472|gb|DR971374.1|DR971374
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|93016578|gb|EB642098.1|EB642098
EST:     GGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: GGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|76283871|gb|DV023439.1|DV023439
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|149088802|gb|EE177929.2|EE177929
EST:     CCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|149000738|gb|EE037956.2|EE037956
EST:     CTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|91877700|gb|EB407657.1|EB407657
EST:     CGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|211192364|gb|FL182432.1|FL182432
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|71431743|gb|DR812793.1|DR812793
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|50333523|gb|CO528649.1|CO528649
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|71426467|gb|DR807517.1|DR807517
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|211194751|gb|FL182433.1|FL182433
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|50325029|gb|CO520155.1|CO520155
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|71766076|gb|DR964013.1|DR964013
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|148960340|gb|EE153599.2|EE153599
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|101383844|gb|EB813977.1|EB813977
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|148960968|gb|EE011664.2|EE011664
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|71433856|gb|DR814906.1|DR814906
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|71439386|gb|DR820436.1|DR820436
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|71312081|gb|DR792563.1|DR792563
EST:     CCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|149077991|gb|EE166727.2|EE166727
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|149084117|gb|EE173519.2|EE173519
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|149012077|gb|EE042497.2|EE042497
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|148967257|gb|EE018458.2|EE018458
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|88757663|gb|DY541804.1|DY541804
EST:     CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTCGCTCGGCTGGTTCCTTCCTTCCTTCCGCTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|148970317|gb|EE021187.2|EE021187
EST:     CTGTGTTCCCTTCTGTTTCT                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: CTGTGTTCCCTTCTGTTTCTgtacgggcgg ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttgatctggccggctgatgaatacgtgcttctctctccgacgaacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGGAGGAGTCCATCGTGGCCGACGGCAACGGCAAGGAGGAAGAGGTCGGGGT
              ggctgat  putative branch site (score: 4)
                   atgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgggcggtgtatatatttttgttttatatcgttgtttggatcttgatctggccggctgatgaatacgtgcttctctctccgacgaacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGGAGGAGTCCATCGTGGCCGACGGCAACGGCAAGGAGGAAGAGGTCGGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG