RetrogeneDB ID: retro_itri_1109

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393377.1:2411921..2412149(+)
• Located in intron of: ENSSTOG00000009822

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFC1
• Ensembl ID: ENSSTOG00000023590
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 1, 6kDa [Source:HGNC Symbol;Acc:7705]

Sequence

>retro_itri_1109
ATGGCACCATCTGTGCTGCTACACCCTTCCTGTGGCTGCTGGCACCCACCAGCCTCCTGAGGGGGGGCCCCTCAGCACGG
TCGGAATTCTACTTGGGGAACTCACCATGTGACAAAGCCGACTGGCTGGAAAGTTGGGTCGACCTTGAGCACCACTGGCT
TCCTGTGGTTCTAGCTCATCCAACCACATAATTAAGATGTTTTAGAGTATAAAAGAAGAAATGGTTTG

Alignment

ORF - retro_itri_1109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 98.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPSALLRH-FSRLLAPARL-PSGACARSKFYLRDPPNDQPDWL-KVGLTLGTTAFLWFYLIKQHDEDVL
          MAPS.LL...F..LLAP..L...G..ARS.FYL...P.D..DWL.KVG.TL.TT.FLWF.LI..H..DVL
Retrocopy MAPSVLLHP<FLWLLAPTSLLRGGPSARSEFYLGNSPCDKADWL>KVGSTLSTTGFLWF*LIQPHN*DVL

Parental  EYKRRNSL
          EYKRRN.L
Retrocopy EYKRRNGL

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_1109 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1109 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 11 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011040	2 retrocopies	retro_amel_282, retro_amel_805,
Bos taurus	ENSBTAG00000039582	2 retrocopies	retro_btau_1578, retro_btau_496,
Dasypus novemcinctus	ENSDNOG00000015639	1 retrocopy	retro_dnov_28,
Echinops telfairi	ENSETEG00000004800	11 retrocopies	retro_etel_1014, retro_etel_1025, retro_etel_135, retro_etel_1735, retro_etel_195, retro_etel_1966, retro_etel_214, retro_etel_670, retro_etel_700, retro_etel_701, retro_etel_87,
Felis catus	ENSFCAG00000008548	1 retrocopy	retro_fcat_146,
Loxodonta africana	ENSLAFG00000010459	5 retrocopies	retro_lafr_1034, retro_lafr_191, retro_lafr_77, retro_lafr_834, retro_lafr_869,
Microcebus murinus	ENSMICG00000006836	1 retrocopy	retro_mmur_771,
Myotis lucifugus	ENSMLUG00000009082	2 retrocopies	retro_mluc_1603, retro_mluc_1660,
Ictidomys tridecemlineatus	ENSSTOG00000023590	3 retrocopies	retro_itri_1087, retro_itri_1109 , retro_itri_1202,
Tursiops truncatus	ENSTTRG00000001107	2 retrocopies	retro_ttru_142, retro_ttru_586,
Vicugna pacos	ENSVPAG00000007703	1 retrocopy	retro_vpac_161,