RetrogeneDB ID: retro_dord_106

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_3263:35603..36107(-)
• Located in intron of: ENSDORG00000008709

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Fkbp3
• Ensembl ID: ENSDORG00000009462
• Aliases: None
• Description: FK506 binding protein 3 [Source:MGI Symbol;Acc:MGI:1353460]

Sequence

>retro_dord_106
CATTTGGTTACAGCCTATAACCATCTCTTTGAAAGTAAGCAGTTTCAAAAGTACTGACAGTATACGTAAAATATCTGAGC
AAGTAAAAAATGTGAAGCTTAATGAAGATAAACCCAAAGAAACCAAGTCTGAAGAGACTCTGGATGAGGGTCCACCAAAA
TATACAAAATTTATTTTTTAAAAAAGGGGGATAAAACAAACTTTCCCAAAAAAGGAGATGTTGTTCACTGCTGGTATACA
GGAACACTACAGGATGGAACTGTTTTTGATTCTAATATTCAAACAAGTTCAAAGAAGAAGAAAAGTGCCAAGACTTTAAG
TTTTAAGGTTGGAGTAGGTAAAGTTACCAGAGGATGGGATGAAGCGCTTTTGACTATGAGTAAAGGAGAAAAGGCTCGAC
TGGAGATTGAACCAGAATGGGCTTATGGGAAGAAAGGACAGCCTGATGCCAAAATTCCACCAAATGCAAAACTTATTTTT
GAAGTGGAATTAGTGGACATCGAT

Alignment

ORF - retro_dord_106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 74.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HLVTAYNHLFESKRF-KGTESISKVSEQVKNVKLNEDKPKETKSEETLDE-GPPK-YTKSILKKGDKTNF
          HLVTAYNHLFESK.F.K.T.SI.K.SEQVKNVKLNEDKPKETKSEETLDE.G..K.Y....LKKGDKTNF
Retrocopy HLVTAYNHLFESKQF>KSTDSIRKISEQVKNVKLNEDKPKETKSEETLDE<GSTKIYKIYFLKKGDKTNF

Parental  PKKGDVVHCWYTGTLQDGTVFDTNIQTSSKKKKSAKPLSFKVGVGKVIRGWDEALLTMSKGEKARLEIEP
          PKKGDVVHCWYTGTLQDGTVFD.NIQTSSKKKKSAK.LSFKVGVGKV.RGWDEALLTMSKGEKARLEIEP
Retrocopy PKKGDVVHCWYTGTLQDGTVFDSNIQTSSKKKKSAKTLSFKVGVGKVTRGWDEALLTMSKGEKARLEIEP

Parental  EWAYGKKGQPDAKIPPNAKLIFEVELVDID
          EWAYGKKGQPDAKIPPNAKLIFEVELVDID
Retrocopy EWAYGKKGQPDAKIPPNAKLIFEVELVDID

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_106 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014018	4 retrocopies	retro_cfam_1788, retro_cfam_440, retro_cfam_616, retro_cfam_798,
Dipodomys ordii	ENSDORG00000009462	1 retrocopy	retro_dord_106 ,
Felis catus	ENSFCAG00000027304	1 retrocopy	retro_fcat_1894,
Loxodonta africana	ENSLAFG00000003572	2 retrocopies	retro_lafr_357, retro_lafr_76,
Macropus eugenii	ENSMEUG00000004962	1 retrocopy	retro_meug_679,
Monodelphis domestica	ENSMODG00000007352	1 retrocopy	retro_mdom_1554,
Otolemur garnettii	ENSOGAG00000003012	2 retrocopies	retro_ogar_2247, retro_ogar_3472,
Tupaia belangeri	ENSTBEG00000006017	13 retrocopies	retro_tbel_1032, retro_tbel_1125, retro_tbel_1696, retro_tbel_1783, retro_tbel_2151, retro_tbel_2569, retro_tbel_3297, retro_tbel_3567, retro_tbel_3807, retro_tbel_4222, retro_tbel_4482, retro_tbel_730, retro_tbel_800,
Tursiops truncatus	ENSTTRG00000006664	1 retrocopy	retro_ttru_1041,