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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagatcatattgcccctgcatgctgtaattctgcaaaataatgttgactaccttttctacatttatcttttttgtgctcatcgatcacattctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGTCTTCCAAAGCATTGGTCCAGTAGAAGGGTGCAAGCTCATCAGAAAAGAA

Basic information

species Zea mays
transcript GRMZM5G835213_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 2
atagatcatattgcccctgcatgctgtaattctgcaaaataatgttgactaccttttctacatttat-cttttttgtgctcatcgatcacattctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGTCTTCCAAAGCATTGGTCCAGTAGAAGGGTGCAAGCTCATCAGAAAAGAA
 |       || |  |   | |  |    | | |||    | ||||| |||  | |||| |||| || |||| || || |   |  | |  |||| ||||||||||||||||||||||||||||||||||||||  || | || || || ||||||||||| ||||||||||||||||| |||||||||||||| || |||
-tgatctggatcgagctctcttcgttatttgcagcattgcattgttggctagatattctgcattcattctttcttatggttgccattgatgttctgaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGATTCACTGCTACATGAGGTCTTCCAAAGTATTGGTCCAGTAGAAGGATGCAAGCTCATCAGGAAGGAA
















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|31361403|gb|CD445760.1|CD445760
EST:     GGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|71328163|gb|DR800724.1|DR800724
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|76916928|gb|DV166611.1|DV166611
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|71449843|gb|DR830893.1|DR830893
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|50328157|gb|CO523283.1|CO523283
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|149005281|gb|EE039830.2|EE039830
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|71764597|gb|DR962534.1|DR962534
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|148944552|gb|EC889676.2|EC889676
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|149096874|gb|EE182668.2|EE182668
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|71428352|gb|DR809402.1|DR809402
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|148965511|gb|EE016330.2|EE016330
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|93013850|gb|EB639370.1|EB639370
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|71760191|gb|DR958128.1|DR958128
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|50322712|gb|CO517838.1|CO517838
EST:     GTCAGGGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|149098619|gb|EE184624.2|EE184624
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|148938880|gb|EC883234.2|EC883234
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|94475248|gb|EB704206.1|EB704206
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|71324258|gb|DR798829.1|DR798829
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|149111090|gb|EE294586.2|EE294586
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|148972836|gb|EE023824.2|EE023824
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|148961382|gb|EE012120.2|EE012120
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|149103764|gb|EE289171.2|EE289171
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|149104833|gb|EE290297.2|EE290297
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|149095084|gb|EE180690.2|EE180690
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|71431558|gb|DR812608.1|DR812608
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|149073417|gb|EE161721.2|EE161721
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|71773943|gb|DR971831.1|DR971831
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|5268356|gb|AI770320.1|AI770320
EST:     CTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: CTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|149079527|gb|EE168509.2|EE168509
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|71756632|gb|DR954569.1|DR954569
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|149004891|gb|EE039402.2|EE039402
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
EST: gi|149084914|gb|EE174423.2|EE174423
EST:     GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT
genomic: GTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttg ... ttctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgactaccttttctacatttatcttttttgtgctcatcgatcacattctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGTCTTCCAAAGCATTGGTCCAGTAGAAGGGTGCAAGCTCATCAGAAAAGAA
 tgttgac  putative branch site (score: 3)
                                           cattctc  putative PPT
        ttttctacatttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagatcatattgcccctgcatgctgtaattctgcaaaataatgttgactaccttttctacatttatcttttttgtgctcatcgatcacattctcaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGACACAGTACTGCAGGAAGTCTTCCAAAGCATTGGTCCAGTAGAAGGGTGCAAGCTCATCAGAAAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - -tgcatgc
- - - - - - - - - - - - - - -ttctgca
- - - - - - - - - - - - - - - - - - - - -atgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctcat