RetrogeneDB ID: retro_itri_1732

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393685.1:464920..465214(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAM16
• Ensembl ID: ENSSTOG00000003461
• Aliases: None
• Description: presequence translocase-associated motor 16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29679]

Sequence

>retro_itri_1732
CAGGAGTTTGCAGCCAGCGGGCCACAGCTGATACCCGGGGACGAGCTGGGCACCCTCTGCAGCTGCATCCAACCCTGCTG
GCCTCGGCCTTCAGGAGGCCCAGCAGATTCTCAGCGTCTCCAAACTGAGTCCCCAGGAGGTCCAGAAGAACTAGGAACAT
CTATTGAAGGTGAACGCTAAACCCTGGGCGGCTCCTTCTACCTACAGTCCAAGGTTGTCGGGTCAAAGGAGCACCTGGAT
GAGGAACTGGGAATCCAGGCCCAGGAGGAGAGAGAGGAAGGGCAGTCACCCAGA

Alignment

ORF - retro_itri_1732 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 79.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QEFAAS-RAAADARGRAGHQ-SAAASNLSGLSLQEAQQILNVSKLSPEEVQKNYEHLFKVNDK-SVGGSF
          QEFAAS.RA.AD.RGRAGH..SAAASN..GL.LQEAQQIL.VSKLSP.EVQKN.EHL.KVN.K...GGSF
Retrocopy QEFAAS<RATADTRGRAGHP<SAAASNPAGLGLQEAQQILSVSKLSPQEVQKN*EHLLKVNAK<TLGGSF

Parental  YLQSKVVRAKERLDEELRIQAQEEKEKEQVPR
          YLQSKVV..KE.LDEEL.IQAQEE.E..Q.PR
Retrocopy YLQSKVVGSKEHLDEELGIQAQEEREEGQSPR

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1732 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1732 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009200	1 retrocopy	retro_btau_1664,
Canis familiaris	ENSCAFG00000019226	1 retrocopy	retro_cfam_1967,
Callithrix jacchus	ENSCJAG00000019772	1 retrocopy	retro_cjac_1148,
Dasypus novemcinctus	ENSDNOG00000010921	2 retrocopies	retro_dnov_1361, retro_dnov_8,
Dipodomys ordii	ENSDORG00000014888	1 retrocopy	retro_dord_81,
Equus caballus	ENSECAG00000019387	1 retrocopy	retro_ecab_302,
Erinaceus europaeus	ENSEEUG00000007432	7 retrocopies	retro_eeur_138, retro_eeur_171, retro_eeur_213, retro_eeur_234, retro_eeur_273, retro_eeur_440, retro_eeur_673,
Echinops telfairi	ENSETEG00000006416	1 retrocopy	retro_etel_2070,
Felis catus	ENSFCAG00000027971	1 retrocopy	retro_fcat_520,
Myotis lucifugus	ENSMLUG00000008921	6 retrocopies	retro_mluc_2446, retro_mluc_2447, retro_mluc_2448, retro_mluc_2516, retro_mluc_2517, retro_mluc_429,
Mus musculus	ENSMUSG00000014301	1 retrocopy	retro_mmus_73,
Rattus norvegicus	ENSRNOG00000004608	1 retrocopy	retro_rnor_713,
Sus scrofa	ENSSSCG00000007947	2 retrocopies	retro_sscr_1090, retro_sscr_468,
Ictidomys tridecemlineatus	ENSSTOG00000003461	1 retrocopy	retro_itri_1732 ,
Tupaia belangeri	ENSTBEG00000001347	1 retrocopy	retro_tbel_3190,
Tarsius syrichta	ENSTSYG00000009306	1 retrocopy	retro_tsyr_282,