RetrogeneDB ID: retro_itri_532

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393299.1:11146698..11147348(+)
• Located in intron of: ENSSTOG00000026157

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A5
• Ensembl ID: ENSSTOG00000020438
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5 [Source:HGNC Symbol;Acc:10991]

Sequence

>retro_itri_532
ATGACAGATGCTGCTGTGTCCTTCGCCAAGGACTTCCTGGCTGGTGGAGTGGCTGCGGCCATCTCCAAGACTGGGGTAGT
GCCCATCGAGCGGGTCAAGCTGCTGTTGCAGGTACAACATGCCTGCAAGCAAATCACTGCAGATAAGCATCACAAGGGCA
TTAGTGACTGTGAGGTTCCTATTCCCAACGAGCAGGCAATCCTGACCTTCTGGCGTGGTAACCTGGCCAATGTCATCAGA
TACTTCCCCACCCAGGCTCTCAACTTTGCCTTCAAAGTTAAATACAAGCAGATCTTCCTGGGTGGTGTGGACAAGAGGAC
CCAGTTTTGGCGCTACTTTGCCGGGAACCTGGCATCAGGTGCTGCTGCAGAGGCCACAACCTTGTGTTTTGTGTACCCTC
TTGATTTTGCCCGAGCCCGCCTAGCAGCTGATATGGGGAAAGCCGGAGCTGAAAGGGAATTCCAAGTCCTCGGTGACTGC
CTGGGTGAGATCTACAAATCTGATGGGATTAAGGGCCTGTACCAGGGCTTTAATGTGTCTGTGCAGGGTATTGTCATCTA
CTGAGCAGCCTACTTTGGTATCTATGACACGCAAAGGGAATGCTTCAGGATCCCAAGAATACTCACATCTCCACCAGCGG
CATGATCGCA

Alignment

ORF - retro_itri_532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.16 %
• Parental protein coverage: 72.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDAAVSFAKDFLAGGVAAAISKTAVAPIERVKLLLQVQHASKQITADKQYKGIIDCVVRIPKEQGILSF
          MTDAAVSFAKDFLAGGVAAAISKT.V.PIERVKLLLQVQHA.KQITADK..KGI.DC.V.IP.EQ.IL.F
Retrocopy MTDAAVSFAKDFLAGGVAAAISKTGVVPIERVKLLLQVQHACKQITADKHHKGISDCEVPIPNEQAILTF

Parental  WRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDKRTQFWRYFAGNLASGGAAGATSLCFVYPLDFARTR
          WRGNLANVIRYFPTQALNFAFK.KYKQIFLGGVDKRTQFWRYFAGNLASG.AA.AT.LCFVYPLDFAR.R
Retrocopy WRGNLANVIRYFPTQALNFAFKVKYKQIFLGGVDKRTQFWRYFAGNLASGAAAEATTLCFVYPLDFARAR

Parental  LAADVGKAGAEREFKGLGDCLVKIYKSDGIKGLYQGFNVSVQGIIIYRAAYFGIYDT-AKGMLPDPKNTH
          LAAD.GKAGAEREF..LGDCL..IYKSDGIKGLYQGFNVSVQGI.IY.AAYFGIYDT.AKGML.DPKNTH
Retrocopy LAADMGKAGAEREFQVLGDCLGEIYKSDGIKGLYQGFNVSVQGIVIY*AAYFGIYDT<AKGMLQDPKNTH

Parental  IFISWMIA
          I..S.MIA
Retrocopy ISTSGMIA

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_532 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_532 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 20 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000143	1 retrocopy	retro_amel_1291,
Canis familiaris	ENSCAFG00000018384	2 retrocopies	retro_cfam_1473, retro_cfam_1641,
Callithrix jacchus	ENSCJAG00000005125	1 retrocopy	retro_cjac_373,
Dasypus novemcinctus	ENSDNOG00000008384	1 retrocopy	retro_dnov_1894,
Echinops telfairi	ENSETEG00000004900	2 retrocopies	retro_etel_23, retro_etel_48,
Felis catus	ENSFCAG00000007057	2 retrocopies	retro_fcat_1035, retro_fcat_127,
Homo sapiens	ENSG00000005022	7 retrocopies	retro_hsap_2243, retro_hsap_3132, retro_hsap_3336, retro_hsap_3516, retro_hsap_3715, retro_hsap_3730, retro_hsap_4239,
Gorilla gorilla	ENSGGOG00000014279	8 retrocopies	retro_ggor_1673, retro_ggor_1674, retro_ggor_2146, retro_ggor_2377, retro_ggor_2512, retro_ggor_2517, retro_ggor_2840, retro_ggor_941,
Loxodonta africana	ENSLAFG00000029398	1 retrocopy	retro_lafr_844,
Microcebus murinus	ENSMICG00000002757	3 retrocopies	retro_mmur_322, retro_mmur_411, retro_mmur_974,
Myotis lucifugus	ENSMLUG00000015742	4 retrocopies	retro_mluc_139, retro_mluc_1580, retro_mluc_2564, retro_mluc_86,
Macaca mulatta	ENSMMUG00000022663	6 retrocopies	retro_mmul_1022, retro_mmul_1287, retro_mmul_1699, retro_mmul_1775, retro_mmul_1800, retro_mmul_2090,
Nomascus leucogenys	ENSNLEG00000014852	7 retrocopies	retro_nleu_131, retro_nleu_1314, retro_nleu_1383, retro_nleu_1679, retro_nleu_2253, retro_nleu_2560, retro_nleu_3105,
Oryctolagus cuniculus	ENSOCUG00000013268	11 retrocopies	retro_ocun_1002, retro_ocun_1233, retro_ocun_1457, retro_ocun_1694, retro_ocun_1705, retro_ocun_1862, retro_ocun_1877, retro_ocun_1890, retro_ocun_1932, retro_ocun_610, retro_ocun_708,
Otolemur garnettii	ENSOGAG00000010008	7 retrocopies	retro_ogar_1131, retro_ogar_1275, retro_ogar_1669, retro_ogar_2161, retro_ogar_2408, retro_ogar_2450, retro_ogar_2474,
Pongo abelii	ENSPPYG00000020669	5 retrocopies	retro_pabe_1006, retro_pabe_2587, retro_pabe_3130, retro_pabe_3141, retro_pabe_3398,
Pteropus vampyrus	ENSPVAG00000014924	2 retrocopies	retro_pvam_1118, retro_pvam_911,
Rattus norvegicus	ENSRNOG00000039980	11 retrocopies	retro_rnor_1242, retro_rnor_1364, retro_rnor_1475, retro_rnor_1612, retro_rnor_1904, retro_rnor_1922, retro_rnor_2533, retro_rnor_2758, retro_rnor_721, retro_rnor_722, retro_rnor_723,
Ictidomys tridecemlineatus	ENSSTOG00000020438	3 retrocopies	retro_itri_314, retro_itri_532 , retro_itri_868,
Tupaia belangeri	ENSTBEG00000006008	4 retrocopies	retro_tbel_1558, retro_tbel_1860, retro_tbel_4654, retro_tbel_4661,