RetrogeneDB ID: retro_dord_115

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_3509:38219..38660(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ap3s2
• Ensembl ID: ENSDORG00000004247
• Aliases: None
• Description: adaptor-related protein complex 3, sigma 2 subunit [Source:MGI Symbol;Acc:MGI:1337060]

Sequence

>retro_dord_115
TTGTGTGGCCTGTGGAGTTACATCCAGTTAATTGGAGGCTCTGACAACAAGCTGATCTACAGACACTATGCAACCCTGTA
GTTTGTCTTCTGTGTGGATTCCTCAGAAAGCGAACTTGGCATTTTAGACCTCATTCAAGTGTTCGTTGGAGACTTAGACA
AATGTTTGGAGAATGTATGTGAGCTGGACTTAATATTCCATGTAGACAAGGTTCACAATATCCTGGCAGAAATGGTGATG
GGCGGAATGGTGCTGGAGACCAACATGAATGAAATTGTCATGCAGATCGATGTGCAGAACAAACTGGAGAAGTCTGAGGC
TGGCTTGGCAGGCGCTCCAGCTCCGGCTGTATCAGCTGTAAAGAATATGAACCTTCCCGAGATCCCAAGAAATATTAACA
TTGGTGACATCAGTATAAAAGTGCCAAACCTGCCCTCTTTT

Alignment

ORF - retro_dord_115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.91 %
• Parental protein coverage: 76.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ICNFLEGGSLIGGSDYKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHMDK
          .C.......LIGGSD.KLIYRHYATL.FVFCVDSSESELGILDLIQVFV..LDKC.ENVCELDLIFH.DK
Retrocopy LCGLWSYIQLIGGSDNKLIYRHYATL*FVFCVDSSESELGILDLIQVFVGDLDKCLENVCELDLIFHVDK

Parental  VHYILQEVVMGGMVLETNMNEIVAQIDAQSRLEKSEGGLSAAPARAVSAVKNINLPEIPRNINLGDLNIK
          VH.IL.E.VMGGMVLETNMNEIV.QID.Q..LEKSE.GL..APA.AVSAVKN.NLPEIPRNIN.GD..IK
Retrocopy VHNILAEMVMGGMVLETNMNEIVMQIDVQNKLEKSEAGLAGAPAPAVSAVKNMNLPEIPRNINIGDISIK

Parental  VPNLSQF
          VPNL..F
Retrocopy VPNLPSF

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_115 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001407	1 retrocopy	retro_btau_436,
Choloepus hoffmanni	ENSCHOG00000003359	4 retrocopies	retro_chof_1775, retro_chof_194, retro_chof_434, retro_chof_88,
Dipodomys ordii	ENSDORG00000004247	1 retrocopy	retro_dord_115 ,
Equus caballus	ENSECAG00000024044	1 retrocopy	retro_ecab_549,
Felis catus	ENSFCAG00000028122	1 retrocopy	retro_fcat_311,
Macropus eugenii	ENSMEUG00000003421	1 retrocopy	retro_meug_2032,
Monodelphis domestica	ENSMODG00000019522	1 retrocopy	retro_mdom_316,
Nomascus leucogenys	ENSNLEG00000011780	2 retrocopies	retro_nleu_1380, retro_nleu_1555,
Otolemur garnettii	ENSOGAG00000030982	1 retrocopy	retro_ogar_1737,
Rattus norvegicus	ENSRNOG00000043141	1 retrocopy	retro_rnor_931,
Sus scrofa	ENSSSCG00000030174	7 retrocopies	retro_sscr_1109, retro_sscr_199, retro_sscr_268, retro_sscr_339, retro_sscr_620, retro_sscr_721, retro_sscr_753,
Tursiops truncatus	ENSTTRG00000015554	2 retrocopies	retro_ttru_1233, retro_ttru_1361,
Vicugna pacos	ENSVPAG00000008668	1 retrocopy	retro_vpac_54,