RetrogeneDB ID: retro_hsap_4901

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:130929681..130930157(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000241418
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM195A
• Ensembl ID: ENSG00000172366
• Aliases: FAM195A, C16orf14, c349E10.1
• Description: family with sequence similarity 195, member A [Source:HGNC Symbol;Acc:14142]

Sequence

>retro_hsap_4901
ATGTACACCATCATCAACGGGCCCAGCAAGTTGGTCGCGCAGCGCCGCACAGGTCTCACGCAGCAGCAGGTGAAGGGCCA
GCTCCAGGAGCTCCTGAAAAGCCGGCAGCCCGCGCCGCCGACCTTGCAGCCCCAGCGGGCGCAGCCCTTCGCGCAGCCGC
TGGGACCCTGGCCCCTGTCGAGTGCAGGGCCAAGGCTTGTGTTCAATCGTGTGAATCGCCGGCGGGACCCCTCCAAGTCC
CCATCCCTCCAGGGGACCCAGGAGACCTACACACTGGCCCACAAGGAGAATGTCCGCTTTGTGTCCGAAGCCTGGCAGCA
GGTGCGGCAGCAGCTGGATGGTGGCCCAGCCGGTGAGGGCGGGACAAGGCCTGTGCAGTGGAGAGGATCCCCAATCCCCG
GCTGCAGAACTTCGTGCCCATTGACTTGGACGAGTGGTGGGCGCAGCACTTCCTGGCTAGAATCACCAGCTGTTCC

Alignment

ORF - retro_hsap_4901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MYTITKGPSKLVAQRRTGPTQQQVEGRLGELLKCRQPAPPTSQPPRAQPFAQPPGPWPLSSPGPRLVFNR
          MYTI..GPSKLVAQRRTG.TQQQV.G.L.ELLK.RQPAPPT.QP.RAQPFAQP.GPWPLSS.GPRLVFNR
Retrocopy MYTIINGPSKLVAQRRTGLTQQQVKGQLQELLKSRQPAPPTLQPQRAQPFAQPLGPWPLSSAGPRLVFNR

Parental  VNGRRAPSTSPSFEGTQETYTVAHEENVRFVSEAWQQVQQQLDGGPAGEGGPRPVQYVERTPNP-RLQNF
          VN.RR.PS.SPS..GTQETYT.AH.ENVRFVSEAWQQV.QQLDGGPAGEGG.RPVQ.....P.P.RLQNF
Retrocopy VNRRRDPSKSPSLQGTQETYTLAHKENVRFVSEAWQQVRQQLDGGPAGEGGTRPVQW-RGSPIP<RLQNF

Parental  VPIDLDEWWAQQFLARITSCS
          VPIDLDEWWAQ.FLARITSCS
Retrocopy VPIDLDEWWAQHFLARITSCS

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	0.00 RPM	2.09 RPM
bodymap2_adrenal	0.00 RPM	6.37 RPM
bodymap2_brain	0.00 RPM	2.88 RPM
bodymap2_breast	0.14 RPM	5.45 RPM
bodymap2_colon	0.00 RPM	8.93 RPM
bodymap2_heart	0.00 RPM	13.44 RPM
bodymap2_kidney	0.00 RPM	15.18 RPM
bodymap2_liver	0.00 RPM	13.44 RPM
bodymap2_lung	0.23 RPM	4.25 RPM
bodymap2_lymph_node	0.00 RPM	8.68 RPM
bodymap2_ovary	0.00 RPM	4.40 RPM
bodymap2_prostate	0.00 RPM	6.15 RPM
bodymap2_skeletal_muscle	0.00 RPM	8.82 RPM
bodymap2_testis	0.02 RPM	9.33 RPM
bodymap2_thyroid	0.00 RPM	6.52 RPM
bodymap2_white_blood_cells	0.02 RPM	2.76 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4901 was not detected

EST

No EST(s) were mapped for retro_hsap_4901 retrocopy.

TSS

No TSS is located nearby retro_hsap_4901 retrocopy 5' end.

Lab

retro_hsap_4901 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4901 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3268

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011979	1 retrocopy	retro_cjac_932,
Homo sapiens	ENSG00000172366	1 retrocopy	retro_hsap_4901 ,
Gorilla gorilla	ENSGGOG00000013784	1 retrocopy	retro_ggor_43,
Nomascus leucogenys	ENSNLEG00000008117	1 retrocopy	retro_nleu_1269,
Pan troglodytes	ENSPTRG00000007548	1 retrocopy	retro_ptro_3268,
Sus scrofa	ENSSSCG00000007995	1 retrocopy	retro_sscr_433,