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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggagtattttctgtgacatatatgtatggagtcaggttacctttgggcttcattttctgtatgcaagatgacttattgttacatgtttgattggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAGTGGCCACAACGAGGTGGAGCTAATGGAAGTTTAAGATTTGATGTTGAGT

Basic information

species Zea mays
transcript GRMZM2G120517_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120517_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g35520.2 (Oryza sativa), 3'ss of exon 2
ggagtattttctgtgacatatatgtatggagtcaggttacctttgggcttca--ttttctgtatgcaagatgacttat-tgttacatgtttgattggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAGTGGCCACAACGAGGTGGAGCTAATGGAAGTTTAAGATTTGATGTTGAGT
    |   |||     | |  ||||    | |||  ||  ||||   || ||  || ||| ||| || | ||  | |  |||||    ||||  || |||||||| ||||| |||||||||||| | ||||||||||||||||||||| | |||||||||||||||||||||||||||||||| || ||||||||||||||||
--gttccattcaaacccttgcatgtgcacaatcaa-ttggctttctactccagtttctctatatccacggtggttaaaatgttattcctttgcctgcatgaagGTTCGTCTTGGATGGCATGATTCCGGTACGTATGACAAGAATATTAAAGAGTGGCCACAACGAGGTGGAGCTAATGGAAGCTTGAGATTTGATGTTGAGT

upper sequence: GRMZM2G120517_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G12020.4 (Glycine max), 3'ss of exon 2
---ggagtattttctgtgacatatatgtatggagtcaggttacctttgggcttcattttctgtatgcaagatgacttattgttacatg--tttgattggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAGTGGCCACAACGAGGTGGAGCTAATGGAAGTTTAAGATTTGATGTTGAGT
   ||| |    |   || |||| || | ||   | |  | |    || | ||  |||||| | |     |  | ||    ||||||   ||| | ||  | | | | ||| | |||||||||||||||||||| ||| | ||||||||||||||||||||||   |||||||||||||||| || ||||||||||| |||||| 
atgggacttgaattcatgtcata-atttttgt--ttatttcattgatgagattt-ttttctatttatttcaatagtttacattacataaatttcaatgtgtta-gATTCGTTTGGGATGGCATGATGCTGGTACATATAATAAGAATATTGAGGAGTGGCCACTGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAGTTGAGC

upper sequence: GRMZM2G120517_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G42720.2 (Glycine max), 3'ss of exon 2
-ggagtattttctgtgacatatatgtatggagtcaggttacctttgggcttcattttctgtatgcaagatgacttattgttacatgtttgattggatga-agGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAGTGGCCACAACGAGGTGGAGCTAATGGAAGTTTAAGATTTGATGTTGAGT
 |  | |  |  |     |||  | |     ||    ||          ||  | |||| | |     |  | ||    ||||||   |  ||  |||  || | ||| | |||||||||||||||||||| ||| | |||||||||||||||||||||||  |||||||||||||||| || |||||||||||  ||||| 
agatgaacctcttacattataacttttgtttgtttcattgatgagattttttttcttctatttatttcaatagtttacattacataaat--ttcaatgtcagATTCGTTTGGGATGGCATGATGCTGGTACTTATAATAAGAATATTGAGGAGTGGCCACAGAGAGGTGGAGCTAATGGTAGCTTAAGATTTGAAATTGAGC

upper sequence: GRMZM2G120517_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT1G77490.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------ggagtattttctgtgacatatatgta-tggagtcaggttacctttgggcttcatt-------ttctgtatgcaagatgacttattgttacatgtttgattggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAGTGGCCACAACGAGGTGGAGCTAATGGAAGTTTAAGATTTGATGTTGAGT
                                    | | |||||      |||  | ||| | |      | |   |         |||       || |||  |  |  |  |||  |||||||||||| |||| |    |||  |  | || ||||| ||||||||||| ||| ||||||||||||||||||||||||   |||||||||||||||||||| | || ||||| | |||| 
gtgaagtatctttctcttcttcatgatgataggacagggaatttttgaattcatggaagtaatagttctttgcttgttactaaagatattggaggaattttgtgagtcatgttgctttgtgttacatgtttcattgca----gGTTAGATTGGGGTGGCACGATGCTGGTACTTATAACAAGAATATTGAGGAGTGGCCACTGAGAGGTGGAGCTAATGGAAGTCTTAGGTTTGAGGCTGAGC

upper sequence: GRMZM2G120517_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0001g02470.t01 (Vitis vinifera), 3'ss of exon 2
-----ggagtattttctgtgacatatatgtatggagtcaggttacctttgggcttcattttctgtatgcaagatgacttattgttacatgtttgattggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAGTGGCCACAACGAGGTGGAGCTAATGGAAGTTTAAGATTTGATGTTGAGT
     |   |  | | | | | | |      |   |  | |||   || |    | |      ||| | ||||||| | |   |     ||||   | ||   |||| || |||||||||||||| || ||||| ||| ||||||| |||||||||||||| | | |||||||||| ||||||||| | ||||||||  ||||| 
tcaaggagatggtctttttaaaaaaacgacctttggatatgtttatttagatgctaagacaaagta-gaaagatgagtaaaaatg----gtttctcttgaaacagGTTCGCCTAGGATGGCATGACGCAGGTACTTATAACAAGAACATTGAGGAGTGGCCTCTAAGAGGTGGAGCAAATGGAAGTCTGAGATTTGAAATTGAGC

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|15177551|gb|BI398490.1|BI398490
EST:     GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTG                         GTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
genomic: GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTGgtgcgtatgg ... ttggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
EST: gi|22489220|gb|BU049143.1|BU049143
EST:     GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTG                         GTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
genomic: GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTGgtgcgtatgg ... ttggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
EST: gi|15188187|gb|BI417164.1|BI417164
EST:     GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTG                         GTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
genomic: GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTGgtgcgtatgg ... ttggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
EST: gi|16137300|gb|BI894165.1|BI894165
EST:     GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTG                         GTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
genomic: GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTGgtgcgtatgg ... ttggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
EST: gi|15323578|gb|BI478812.1|BI478812
EST:     GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTG                         GTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
genomic: GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTGgtgcgtatgg ... ttggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
EST: gi|15323577|gb|BI478811.1|BI478811
EST:     GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTG                         GTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
genomic: GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTGgtgcgtatgg ... ttggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
EST: gi|89106264|gb|DY576481.1|DY576481
EST:     GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTG                         GTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
genomic: GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTGgtgcgtatgg ... ttggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
EST: gi|15177552|gb|BI398491.1|BI398491
EST:     GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTG                         GTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
genomic: GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTGgtgcgtatgg ... ttggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
EST: gi|16137301|gb|BI894166.1|BI894166
EST:     GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTG                         GTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
genomic: GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTGgtgcgtatgg ... ttggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
EST: gi|18383818|gb|BM417018.1|BM417018
EST:     GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTG                         GTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
genomic: GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTGgtgcgtatgg ... ttggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
EST: gi|22489146|gb|BU049069.1|BU049069
EST:     GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTG                         GTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG
genomic: GCGAGGACATCAGGGAGCTTCTCAGGACGACTCACTCCCACCCCATCCTGgtgcgtatgg ... ttggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcttcattttctgtatgcaagatgacttattgttacatgtttgattggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAGTGGCCACAACGAGGTGGAGCTAATGGAAGTTTAAGATTTGATGTTGAGT
                                       gtttgat  putative branch site (score: 5)
                           ttattgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggagtattttctgtgacatatatgtatggagtcaggttacctttgggcttcattttctgtatgcaagatgacttattgttacatgtttgattggatgaagGTCCGTCTAGGATGGCATGATGCTGGTACGTATGACAAGAATATTGAGGAGTGGCCACAACGAGGTGGAGCTAATGGAAGTTTAAGATTTGATGTTGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG