RetrogeneDB ID: retro_hsap_2742

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:194476317..194477256(+)
• Located in intron of: ENSG00000237222

Retrocopy information

• Ensembl ID: ENSG00000234805
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM151A
• Ensembl ID: ENSG00000162391
• Aliases: FAM151A, C1orf179
• Description: family with sequence similarity 151, member A [Source:HGNC Symbol;Acc:25032]

Sequence

>retro_hsap_2742
ATGGCCTGCAGGGAGCAGTTATCGAAGAATCAGGTCAAGTGGGGGTTTGCTGGCATTACCTGTGTTTCTGTAGTGGTCAT
TGCCGCGATAGTCCTTGCCATCGCCTTGCGGTGGCCAGGCTGTGAGCTGGAGGCCTGCAGCTCCGAGGCCGACATGCTGG
ATTACCTGCTGAGCCTGGGCCAGATCAGCTGCCGAGATGCCCTGGAGGTCACCTGGTACCACGCAGCCAACAGCAAGAAA
GCCGTGACAGCTGCCCTGAACAGCAACATCACAGTCCTGGAGGCTGACGTCAATGTAGAAGGGCTCGGCACAGCTGACGA
GACAGGAGCTCCCATCGTGGCACACCCTCCGGCTATCTACAGTGATGACACACTGGAGCAGTGGCTGGATGGTGTGCTGG
GCTCTTCCCAGAAGGGCATCAAACTGGACTTCAAGAACATCAAGGCCGTGGGCCCCTCCCTGGACCTCCTGTGGTAGCTG
ACAGAGTGGGGCAAAGTCCGGCGGCCCATGTGGATCAACGCTGACATCTTAAAGGGCCCCGACATGCCCATCTCAGCTGA
GGTCAGTGCCACACAGTTCCTGGCCCTGGTCCAGGAGAAGTATCCCAAGGCCACCCTGTCTCCAGGCTGGACCACCCTGT
ACGTGCCCATGTTCCCAAACAGGACGTACACCCGAGCCATGGTGGAGAAGATGCACGAGCTGGTGGGAGTGGTGCTCCAG
AGGGTCACCTTCCCTGTGCGGTCTTCCACAGTGCGGGCCGCCCAGGCCCACTCCAGCTGGCTGCTGAGCCAATCTGAGAG
GTACAGCCTGACGCTATGGCAGGCTGCCTCGGACCCCATGTTGGCAGAGGATCTGCCCTACGTCCAGGATAACACTGCTG
TCCACCACGTCTACTGTGATATCTTTGAGCCTTTCCTGTTGCAGTTCAAGCAGGTGGCC

Alignment

ORF - retro_hsap_2742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.26 %
• Parental protein coverage: 53.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVCREQLSKNQVKWVFAGITCVSVVVIAAIVLAITLRRPGCELEACSPDADMLDYLLSLGQISRRDALEV
          M.CREQLSKNQVKW.FAGITCVSVVVIAAIVLAI.LR.PGCELEACS..ADMLDYLLSLGQIS.RDALEV
Retrocopy MACREQLSKNQVKWGFAGITCVSVVVIAAIVLAIALRWPGCELEACSSEADMLDYLLSLGQISCRDALEV

Parental  TWYHAANSKKAMTAALNSNITVLEADVNVEGLGTANETGVPIMAHPPTIYSDNTLEQWLDAVLGSSQKGI
          TWYHAANSKKA.TAALNSNITVLEADVNVEGLGTA.ETG.PI.AHPP.IYSD.TLEQWLD.VLGSSQKGI
Retrocopy TWYHAANSKKAVTAALNSNITVLEADVNVEGLGTADETGAPIVAHPPAIYSDDTLEQWLDGVLGSSQKGI

Parental  KLDFKNIKAVGPSLDLLRQLTEEGKVRRPIWINADILKGPNMLISTEVNATQFLALVQEKYPKATLSPGW
          KLDFKNIKAVGPSLDLL..LTE.GKVRRP.WINADILKGP.M.IS.EV.ATQFLALVQEKYPKATLSPGW
Retrocopy KLDFKNIKAVGPSLDLLW*LTEWGKVRRPMWINADILKGPDMPISAEVSATQFLALVQEKYPKATLSPGW

Parental  TTFYMSTSPNRTYTQAMVEKMHELVGGVPQRVTFPVRSSMVRAAWPHFSWLLSQSERYSLTLWQAASDPM
          TT.Y....PNRTYT.AMVEKMHELVG.V.QRVTFPVRSS.VRAA..H.SWLLSQSERYSLTLWQAASDPM
Retrocopy TTLYVPMFPNRTYTRAMVEKMHELVGVVLQRVTFPVRSSTVRAAQAHSSWLLSQSERYSLTLWQAASDPM

Parental  SVEDLLYVRDNTAVHQVYYDIFEPLLSQFKQLA
          ..EDL.YV.DNTAVH.VY.DIFEP.L.QFKQ.A
Retrocopy LAEDLPYVQDNTAVHHVYCDIFEPFLLQFKQVA

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	0.00 RPM
bodymap2_adrenal	0.00 RPM	2.39 RPM
bodymap2_brain	0.00 RPM	0.91 RPM
bodymap2_breast	0.00 RPM	0.33 RPM
bodymap2_colon	0.00 RPM	1.88 RPM
bodymap2_heart	0.00 RPM	1.99 RPM
bodymap2_kidney	0.00 RPM	20.64 RPM
bodymap2_liver	0.00 RPM	1.10 RPM
bodymap2_lung	0.00 RPM	0.07 RPM
bodymap2_lymph_node	0.00 RPM	1.15 RPM
bodymap2_ovary	0.00 RPM	1.08 RPM
bodymap2_prostate	0.00 RPM	0.62 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.02 RPM	0.45 RPM
bodymap2_thyroid	0.09 RPM	1.28 RPM
bodymap2_white_blood_cells	0.00 RPM	0.12 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2742 was not detected

EST

No EST(s) were mapped for retro_hsap_2742 retrocopy.

TSS

No TSS is located nearby retro_hsap_2742 retrocopy 5' end.

Lab

retro_hsap_2742 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2742 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1489

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019801	1 retrocopy	retro_btau_325,
Homo sapiens	ENSG00000162391	1 retrocopy	retro_hsap_2742 ,
Myotis lucifugus	ENSMLUG00000014446	1 retrocopy	retro_mluc_965,
Macaca mulatta	ENSMMUG00000013680	1 retrocopy	retro_mmul_1489,
Pongo abelii	ENSPPYG00000001314	1 retrocopy	retro_pabe_2276,