RetrogeneDB ID: retro_hsap_2232

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:20729229..20729736(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAF2
• Ensembl ID: ENSG00000164182
• Aliases: NDUFAF2, B17.2L, MMTN, NDUFA12L, mimitin
• Description: NADH dehydrogenase (ubiquinone) complex I, assembly factor 2 [Source:HGNC Symbol;Acc:28086]

Sequence

>retro_hsap_2232
ATGGGTTGGTCTCAGGATTTGTTCCGCGCCTTGTGGAGATCGCTGTCAAGGGAAGTGAAGGAGCACGTGGGCACGGACCA
ATTCGGGAACAAATACTACTACATCCTGCAGAACAAGAACTGGAGAGGACAAACTATTCAAGAGAAAAGAATTGTAGAAG
CAGCAAATAAAAAAGAAGTAGACTATGAAACAGGGGATATTCCAACAGAATGGGAAGCTTGGATTAGAAGAACAAGAAAG
ACTCCACCTACTATGGAGGAAATACTAAAGAATGAAAAACACAGAGAAGAAATCAAAATAAAAAGCCAAGATTTTTATGA
AAAAGAAAAACTCCTTAGTAAAGAGACCAGTGAGGAACTCCTGCCTCCACCAGTTCAAACTCAAATTAAAGGCCGTGCCT
CTGCTCCATACTTCGGAAAGGAAAAACCCTCAGTGGCTCCCAGCAGCACTGGTAAAACCTTTCAGCCAGGATCCTGGATG
CCACGAGATGGCAAGAGCCACAATGAA

Alignment

ORF - retro_hsap_2232 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGWSQDLFRALWRSLSREVKEHVGTDQFGNKYYYIPQYKNWRGQTIREKRIVEAANKKEVDYEAGDIPTE
          MGWSQDLFRALWRSLSREVKEHVGTDQFGNKYYYI.Q.KNWRGQTI.EKRIVEAANKKEVDYE.GDIPTE
Retrocopy MGWSQDLFRALWRSLSREVKEHVGTDQFGNKYYYILQNKNWRGQTIQEKRIVEAANKKEVDYETGDIPTE

Parental  WEAWIRRTRKTPPTMEEILKNEKHREEIKIKSQDFYEKEKLLSKETSEELLPPPVQTQIKGHASAPYFGK
          WEAWIRRTRKTPPTMEEILKNEKHREEIKIKSQDFYEKEKLLSKETSEELLPPPVQTQIKG.ASAPYFGK
Retrocopy WEAWIRRTRKTPPTMEEILKNEKHREEIKIKSQDFYEKEKLLSKETSEELLPPPVQTQIKGRASAPYFGK

Parental  EEPSVAPSSTGKTFQPGSWMPRDGKSHNQ
          E.PSVAPSSTGKTFQPGSWMPRDGKSHN.
Retrocopy EKPSVAPSSTGKTFQPGSWMPRDGKSHNE

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.52 RPM	9.60 RPM
bodymap2_adrenal	1.00 RPM	10.46 RPM
bodymap2_brain	0.35 RPM	13.24 RPM
bodymap2_breast	1.17 RPM	9.46 RPM
bodymap2_colon	0.35 RPM	20.15 RPM
bodymap2_heart	0.11 RPM	11.21 RPM
bodymap2_kidney	0.14 RPM	13.46 RPM
bodymap2_liver	0.36 RPM	8.81 RPM
bodymap2_lung	0.35 RPM	12.82 RPM
bodymap2_lymph_node	0.00 RPM	9.90 RPM
bodymap2_ovary	0.85 RPM	12.20 RPM
bodymap2_prostate	0.36 RPM	20.71 RPM
bodymap2_skeletal_muscle	0.04 RPM	12.46 RPM
bodymap2_testis	0.47 RPM	20.61 RPM
bodymap2_thyroid	0.85 RPM	10.71 RPM
bodymap2_white_blood_cells	0.24 RPM	6.91 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2232 was not detected

EST

No EST(s) were mapped for retro_hsap_2232 retrocopy.

TSS

No TSS is located nearby retro_hsap_2232 retrocopy 5' end.

Lab

retro_hsap_2232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2232 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013975	2 retrocopies	retro_chof_1922, retro_chof_733,
Callithrix jacchus	ENSCJAG00000015375	1 retrocopy	retro_cjac_3153,
Homo sapiens	ENSG00000164182	1 retrocopy	retro_hsap_2232 ,