RetrogeneDB ID: retro_hsap_3744

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:65163546..65163962(+)
• Located in intron of: ENSG00000232270

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM162B
• Ensembl ID: ENSG00000183807
• Aliases: FAM162B, C6orf189, bA86F4.2
• Description: family with sequence similarity 162, member B [Source:HGNC Symbol;Acc:21549]

Sequence

>retro_hsap_3744
TGTGCCCCTGGGAAGCCTCTAGAAGCCACACAGAGGCCCATAGCAACTCTCATGCCCTGGAGGGTCTCACCAGCCACTCC
AGTGATGGGCCCTCCAGTAGCTCTGGGACCCAAGCAGGGATGATTCACAAAGTCCCTACCGAGCACAGGCCTTCACAGTT
CAACAAGAAAATCCTACTGTTGACTGGATTTTTAAAAATCAGTGGAGGAGATCACACTAGAAATGATAGATATTGCAAGA
AACAAAGCTTGAGGGAAAGCTTGTTACCGTAATGAATGGACTCACACATATCACTGCTTTGCAGTGATAGCATCAGCCAA
AAGGGCTGCGAACATGAATCATTAACAAGTTGAAATATGTCAAAGATGGCTGTGTGGTGTGAAGAAGCTGCATTAGCTGC
ACAGGCTAAGGCTAAA

Alignment

ORF - retro_hsap_3744 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.33 %
• Parental protein coverage: 88.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  CGPGAPLEATRRP-APALPPR-GLPCYSSGGAPSNSGPQGHGEIHRVPTQRRPSQFDKKILLWTGRFK-S
          C.PG.PLEAT.RP.A...P.R.GL...SS.G..S.SG.Q..G.IH.VPT..RPSQF.KKILL.TG..K.S
Retrocopy CAPGKPLEATQRPIATLMPWR<GLTSHSSDGPSSSSGTQA-GMIHKVPTEHRPSQFNKKILLLTGFLK>S

Parental  MEEIPPRIPPEMIDTARNKARVKACY-IMIGLTIIA-CFAVIVS-AKRAVERHESLTSWNLAKKAKWREE
          .EE....I..EMID.ARNKA..KACY..M.GLT.I..CFAVI.S......E.HESLTS.N..K.A.W.EE
Retrocopy VEE----ITLEMIDIARNKA*GKACY>VMNGLTHIT<CFAVIAS<SQKGCE-HESLTS*NMSKMAVWCEE

Parental  AALAAQAKAK
          AALAAQAKAK
Retrocopy AALAAQAKAK

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	0.02 RPM	4.21 RPM
bodymap2_adrenal	0.06 RPM	7.45 RPM
bodymap2_brain	0.07 RPM	1.38 RPM
bodymap2_breast	0.00 RPM	3.42 RPM
bodymap2_colon	0.21 RPM	6.54 RPM
bodymap2_heart	0.00 RPM	2.62 RPM
bodymap2_kidney	0.10 RPM	2.61 RPM
bodymap2_liver	0.00 RPM	0.02 RPM
bodymap2_lung	0.00 RPM	15.72 RPM
bodymap2_lymph_node	0.00 RPM	8.88 RPM
bodymap2_ovary	0.44 RPM	3.57 RPM
bodymap2_prostate	0.29 RPM	6.72 RPM
bodymap2_skeletal_muscle	0.00 RPM	1.46 RPM
bodymap2_testis	0.08 RPM	3.79 RPM
bodymap2_thyroid	0.00 RPM	2.07 RPM
bodymap2_white_blood_cells	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3744 was not detected

EST

No EST(s) were mapped for retro_hsap_3744 retrocopy.

TSS

No TSS is located nearby retro_hsap_3744 retrocopy 5' end.

Lab

retro_hsap_3744 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3744 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2542
Pan troglodytes	retro_ptro_2994
Pan troglodytes	retro_ptro_2541

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000183807	2 retrocopies	retro_hsap_3744 , retro_hsap_901,
Gorilla gorilla	ENSGGOG00000002045	1 retrocopy	retro_ggor_728,
Microcebus murinus	ENSMICG00000014555	1 retrocopy	retro_mmur_746,
Mus musculus	ENSMUSG00000019909	1 retrocopy	retro_mmus_2292,
Pan troglodytes	ENSPTRG00000018538	4 retrocopies	retro_ptro_2541, retro_ptro_2542, retro_ptro_2994, retro_ptro_621,