RetrogeneDB ID: retro_itri_916

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393344.1:7610694..7611066(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAB1
• Ensembl ID: ENSSTOG00000024657
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa [Source:HGNC Symbol;Acc:7694]

Sequence

>retro_itri_916
GCCACCCAGCTGGGTGTCCCGGGGAACTAGACAAGGCCCGGGACTAAGCAGCCAGCCTTACTGCTCATGAAGATTCCATG
GAGAGTCACACCGTTGTGCCATCAGTATAGTGACACAACCCTTTTGACGTTAGAGAAAATTAAGGACCGTGTTTTGTACG
TCCTGAAACTCCATGATAAGACTGACCCAGAAAAGCTTTCGGTAAATTCTCATTGTATGAAAGACCTGGGCTTAGACGGT
TTGGACCAAGTGGAGATTACCATGGCCATAGAAGGCGAATTTGGGTTTGAAATTCCTGATACAGAGGCAGAAAAGTTAAT
GTGTCCACAAGCAACTGTTGATTACATTACAGATAAGAAGGATGTACACGAA

Alignment

ORF - retro_itri_916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.39 %
• Parental protein coverage: 79.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STALCPAGNRTWPGTTQLALVLTQVPGRVTQLCRQYSDAPPLTLEGIKDRVLYVLKLYDKIDPEKLSVNS
          .T.L...GN.T.PGT.Q.AL.L...P.RVT.LC.QYSD...LTLE.IKDRVLYVLKL.DK.DPEKLSVNS
Retrocopy ATQLGVPGN*TRPGTKQPALLLMKIPWRVTPLCHQYSDTTLLTLEKIKDRVLYVLKLHDKTDPEKLSVNS

Parental  HFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYE
          H.MKDLGLD.LDQVEI.MA.E.EFGFEIPD..AEKLMCPQ..VDYI.DKKDV.E
Retrocopy HCMKDLGLDGLDQVEITMAIEGEFGFEIPDTEAEKLMCPQATVDYITDKKDVHE

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_916 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_916 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 17 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014304	1 retrocopy	retro_amel_1692,
Canis familiaris	ENSCAFG00000017667	3 retrocopies	retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Callithrix jacchus	ENSCJAG00000020616	2 retrocopies	retro_cjac_2635, retro_cjac_3099,
Cavia porcellus	ENSCPOG00000012038	2 retrocopies	retro_cpor_728, retro_cpor_767,
Felis catus	ENSFCAG00000013241	3 retrocopies	retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Homo sapiens	ENSG00000004779	1 retrocopy	retro_hsap_3484,
Gorilla gorilla	ENSGGOG00000006320	1 retrocopy	retro_ggor_2349,
Macropus eugenii	ENSMEUG00000012681	3 retrocopies	retro_meug_1780, retro_meug_303, retro_meug_830,
Microcebus murinus	ENSMICG00000007778	2 retrocopies	retro_mmur_1193, retro_mmur_120,
Macaca mulatta	ENSMMUG00000020522	1 retrocopy	retro_mmul_101,
Monodelphis domestica	ENSMODG00000016352	1 retrocopy	retro_mdom_389,
Mus musculus	ENSMUSG00000030869	6 retrocopies	retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947, retro_mmus_3094, retro_mmus_3332,
Otolemur garnettii	ENSOGAG00000005562	2 retrocopies	retro_ogar_2916, retro_ogar_325,
Pongo abelii	ENSPPYG00000007192	1 retrocopy	retro_pabe_2879,
Pan troglodytes	ENSPTRG00000007889	1 retrocopy	retro_ptro_2358,
Rattus norvegicus	ENSRNOG00000018129	2 retrocopies	retro_rnor_1353, retro_rnor_2058,
Ictidomys tridecemlineatus	ENSSTOG00000024657	2 retrocopies	retro_itri_281, retro_itri_916 ,