RetrogeneDB ID: retro_itri_1368

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393459.1:3853491..3854041(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIP7
• Ensembl ID: ENSSTOG00000012871
• Aliases: None
• Description: NIP7, nucleolar pre-rRNA processing protein [Source:HGNC Symbol;Acc:24328]

Sequence

>retro_itri_1368
ATGCGGCCTTTGACTGAGTAGGAGACCCATGTAACATTTGAGAAGATAGCCAAATACATCCAGGAGAATCTTCAGCTATT
GGTCCTCAGGCCAGATGGCACCTACTGTTTCAGGCTACACAACAGCCAGGTGTACTATATTAGTGAGAAGATTTTGAAGC
TGGCCACCAGTATCTCAGGGTACAAGTTGGTGTCCCTGGGACCTGCTTTCGAAAATTCACTAAGGCCCACAATTCCCATT
GTGAATACAGTGAATACAGCTCTGGATTACCTGTATTTGCACCCTATACCAAGTATAAAGTATGAATAAAGCTCAGAGTA
GAGCAGTCCTTCTGTACAGAAACCATGTGTTGAAATATGGTCTCGGTTAAATCATTGAAAACACTTCTCAATACCAGGAA
GTGGTGGTGTCCACCGTGGCAGAAATTCCTTTGGGTTTTGCTAAAGCGTCAAAGTCTACACAAGACTGCAGGAAAGAAAA
CCCCATAGTGATTGCGGTATTTCTTCAAGCAGACATTGGGGAATATGTACAGCATGAAGAGACATTGACT

Alignment

ORF - retro_itri_1368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRPLTEEETRVMFEKIAKYIGENLQLLVDRPDGTYCFRLHNDRVYYVSEKILKLAANISGDKLVSL-GTC
          MRPLTE.ET.V.FEKIAKYI.ENLQLLV.RPDGTYCFRLHN..VYY.SEKILKLA..ISG.KLVSL.GTC
Retrocopy MRPLTE*ETHVTFEKIAKYIQENLQLLVLRPDGTYCFRLHNSQVYYISEKILKLATSISGYKLVSL<GTC

Parental  FGKFTKTH----KFRLHITALDYLAPYAKYKVWIKPGAEQSF-LYGNHVLKSGLGRITENTSQYQGVVVY
          F.KFTK.H............L...APY.KYKV.IK...EQSF.LY.NHVLK.GLG.I.ENTSQYQ.VVV.
Retrocopy FRKFTKAHNSHCEYSEYSSGLPVFAPYTKYKV*IKLRVEQSF<LYRNHVLKYGLG*IIENTSQYQEVVVS

Parental  SMADIPLGFGVAAKSTQDCRKVDPMAIVVFHQADIGEYVRHEETLT
          ..A.IPLGF..A.KSTQDCRK..P..I.VF.QADIGEYV.HEETLT
Retrocopy TVAEIPLGFAKASKSTQDCRKENPIVIAVFLQADIGEYVQHEETLT

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_1368 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1368 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 21 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007542	1 retrocopy	retro_amel_938,
Bos taurus	ENSBTAG00000001666	1 retrocopy	retro_btau_353,
Canis familiaris	ENSCAFG00000029835	2 retrocopies	retro_cfam_1346, retro_cfam_1682,
Callithrix jacchus	ENSCJAG00000015364	2 retrocopies	retro_cjac_2466, retro_cjac_4212,
Dasypus novemcinctus	ENSDNOG00000006821	2 retrocopies	retro_dnov_2114, retro_dnov_74,
Homo sapiens	ENSG00000132603	2 retrocopies	retro_hsap_2707, retro_hsap_3648,
Gorilla gorilla	ENSGGOG00000022785	2 retrocopies	retro_ggor_1886, retro_ggor_2464,
Microcebus murinus	ENSMICG00000009664	1 retrocopy	retro_mmur_5,
Myotis lucifugus	ENSMLUG00000011835	3 retrocopies	retro_mluc_1119, retro_mluc_2171, retro_mluc_2508,
Macaca mulatta	ENSMMUG00000016635	2 retrocopies	retro_mmul_1801, retro_mmul_192,
Monodelphis domestica	ENSMODG00000002782	2 retrocopies	retro_mdom_1011, retro_mdom_1709,
Mus musculus	ENSMUSG00000031917	2 retrocopies	retro_mmus_1858, retro_mmus_2281,
Nomascus leucogenys	ENSNLEG00000005492	2 retrocopies	retro_nleu_1579, retro_nleu_510,
Oryctolagus cuniculus	ENSOCUG00000017652	5 retrocopies	retro_ocun_1013, retro_ocun_1262, retro_ocun_1292, retro_ocun_491, retro_ocun_721,
Otolemur garnettii	ENSOGAG00000008066	2 retrocopies	retro_ogar_1619, retro_ogar_2453,
Pongo abelii	ENSPPYG00000007503	2 retrocopies	retro_pabe_2258, retro_pabe_2995,
Pan troglodytes	ENSPTRG00000008279	2 retrocopies	retro_ptro_1828, retro_ptro_2473,
Rattus norvegicus	ENSRNOG00000020391	8 retrocopies	retro_rnor_1279, retro_rnor_1566, retro_rnor_1567, retro_rnor_1674, retro_rnor_1676, retro_rnor_485, retro_rnor_655, retro_rnor_865,
Sorex araneus	ENSSARG00000000303	1 retrocopy	retro_sara_665,
Ictidomys tridecemlineatus	ENSSTOG00000012871	1 retrocopy	retro_itri_1368 ,
Tursiops truncatus	ENSTTRG00000010012	2 retrocopies	retro_ttru_1783, retro_ttru_676,