RetrogeneDB ID: retro_hsap_1485

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:41455963..41456545(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000157021
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM92A1
• Ensembl ID: ENSG00000188343
• Aliases: None
• Description: family with sequence similarity 92, member A1 [Source:HGNC Symbol;Acc:30452]

Sequence

>retro_hsap_1485
GTAGTTGAACCCTTGAAAGCTTATGGGACCATTGTGAAAATGAAACGGGATGACCTCAAAGCAACATTCACAGCAAGGAA
TCGAGAAGCTAAGCAATTAACTCAGTTAGAAAGAACACGTCAGCGAAACCCATCTGATCGACATGTTATTTCACAGGCAG
AAACGGAATTACAGAGAACTGCAATGGATGCTAGCCGAACAAGTCGTCATCTGGAGGAAACTATTAACAACTTTGAAAGG
CAGAAAATGAAGGATATAAAGACTATATTTTCTGAATTTATCACAATCGAAATGTTATTTCACGGCAAAGCTTTAGAGGT
CTACACTGCTGCCTACCGGAATATACAAAACATTGATGAAGATGAAGATTTAGAGGTTTTCCGAAATTCTCTGTATGCAC
CAGATTATTCATCTTGTTTAGATACTGTAAGAGCGAATTCAAAGTCACCTCTTCAGAGATCACTGTCAGCTAAGTGTGTA
TCTGGAACAAGACAGGTATCCACTTGTCGACTAAGAAAGGATCAACAAGCAGAAGATGATGAGGATGAAGAGTTAGATGT
TACAGAAGAAGAAAATTTTCTT

Alignment

ORF - retro_hsap_1485 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.88 %
• Parental protein coverage: 67.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVEPLKTYGTIVKMKRDDLKATLTARNREAKQLTQLERTRQRNPSDRHVISQAETELQRAAMDASRTSRH
          VVEPLK.YGTIVKMKRDDLKAT.TARNREAKQLTQLERTRQRNPSDRHVISQAETELQR.AMDASRTSRH
Retrocopy VVEPLKAYGTIVKMKRDDLKATFTARNREAKQLTQLERTRQRNPSDRHVISQAETELQRTAMDASRTSRH

Parental  LEETINNFERQKMKDIKTIFSEFITIEMLFHGKALEVYTAAYQNIQNIDEDEDLEVFRNSLYAPDYSSRL
          LEETINNFERQKMKDIKTIFSEFITIEMLFHGKALEVYTAAY.NIQNIDEDEDLEVFRNSLYAPDYSS.L
Retrocopy LEETINNFERQKMKDIKTIFSEFITIEMLFHGKALEVYTAAYRNIQNIDEDEDLEVFRNSLYAPDYSSCL

Parental  DIVRANSKSPLQRSLSAKCVSGTGQVSTCRLRKDQQAEDDEDDELDVTEEENFL
          D.VRANSKSPLQRSLSAKCVSGT.QVSTCRLRKDQQAEDDED.ELDVTEEENFL
Retrocopy DTVRANSKSPLQRSLSAKCVSGTRQVSTCRLRKDQQAEDDEDEELDVTEEENFL

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	0.12 RPM	16.22 RPM
bodymap2_adrenal	0.02 RPM	16.25 RPM
bodymap2_brain	0.33 RPM	25.81 RPM
bodymap2_breast	0.08 RPM	26.95 RPM
bodymap2_colon	0.27 RPM	21.97 RPM
bodymap2_heart	0.37 RPM	23.59 RPM
bodymap2_kidney	0.45 RPM	35.53 RPM
bodymap2_liver	0.36 RPM	10.33 RPM
bodymap2_lung	0.04 RPM	11.78 RPM
bodymap2_lymph_node	0.11 RPM	13.43 RPM
bodymap2_ovary	0.27 RPM	34.97 RPM
bodymap2_prostate	0.33 RPM	26.41 RPM
bodymap2_skeletal_muscle	0.00 RPM	4.78 RPM
bodymap2_testis	0.26 RPM	90.21 RPM
bodymap2_thyroid	0.00 RPM	25.12 RPM
bodymap2_white_blood_cells	0.00 RPM	7.97 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1485 was not detected

EST

No EST(s) were mapped for retro_hsap_1485 retrocopy.

TSS

No TSS is located nearby retro_hsap_1485 retrocopy 5' end.

Lab

retro_hsap_1485 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1485 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1137

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009105	1 retrocopy	retro_cfam_1072,
Echinops telfairi	ENSETEG00000013003	1 retrocopy	retro_etel_522,
Homo sapiens	ENSG00000188343	1 retrocopy	retro_hsap_1485 ,
Gorilla gorilla	ENSGGOG00000006452	1 retrocopy	retro_ggor_1137,
Loxodonta africana	ENSLAFG00000003954	1 retrocopy	retro_lafr_201,
Microcebus murinus	ENSMICG00000006797	1 retrocopy	retro_mmur_415,
Monodelphis domestica	ENSMODG00000007447	2 retrocopies	retro_mdom_1239, retro_mdom_827,
Mustela putorius furo	ENSMPUG00000009112	1 retrocopy	retro_mputfur_1183,
Nomascus leucogenys	ENSNLEG00000002773	1 retrocopy	retro_nleu_1707,
Otolemur garnettii	ENSOGAG00000002972	1 retrocopy	retro_ogar_654,
Oreochromis niloticus	ENSONIG00000002446	1 retrocopy	retro_onil_57,
Procavia capensis	ENSPCAG00000011171	1 retrocopy	retro_pcap_272,
Pongo abelii	ENSPPYG00000018744	2 retrocopies	retro_pabe_1235, retro_pabe_2497,
Tarsius syrichta	ENSTSYG00000012502	1 retrocopy	retro_tsyr_975,
Tursiops truncatus	ENSTTRG00000012378	1 retrocopy	retro_ttru_45,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.41 RPM
CEU_NA11843	0.65 RPM
CEU_NA11930	0.65 RPM
CEU_NA12004	0.61 RPM
CEU_NA12400	0.84 RPM
CEU_NA12751	0.73 RPM
CEU_NA12760	0.36 RPM
CEU_NA12827	1.18 RPM
CEU_NA12872	0.60 RPM
CEU_NA12873	0.89 RPM
FIN_HG00183	0.96 RPM
FIN_HG00277	0.30 RPM
FIN_HG00315	0.75 RPM
FIN_HG00321	0.79 RPM
FIN_HG00328	0.31 RPM
FIN_HG00338	0.75 RPM
FIN_HG00349	1.17 RPM
FIN_HG00375	0.51 RPM
FIN_HG00377	0.71 RPM
FIN_HG00378	0.32 RPM
GBR_HG00099	0.44 RPM
GBR_HG00111	0.69 RPM
GBR_HG00114	0.66 RPM
GBR_HG00119	0.91 RPM
GBR_HG00131	0.55 RPM
GBR_HG00133	0.70 RPM
GBR_HG00134	0.48 RPM
GBR_HG00137	0.36 RPM
GBR_HG00142	0.61 RPM
GBR_HG00143	0.35 RPM
TSI_NA20512	0.17 RPM
TSI_NA20513	0.46 RPM
TSI_NA20518	0.42 RPM
TSI_NA20532	0.44 RPM
TSI_NA20538	0.55 RPM
TSI_NA20756	0.99 RPM
TSI_NA20765	0.06 RPM
TSI_NA20771	0.77 RPM
TSI_NA20786	0.42 RPM
TSI_NA20798	0.37 RPM
YRI_NA18870	0.17 RPM
YRI_NA18907	0.52 RPM
YRI_NA18916	0.82 RPM
YRI_NA19093	0.23 RPM
YRI_NA19099	0.56 RPM
YRI_NA19114	0.73 RPM
YRI_NA19118	0.41 RPM
YRI_NA19213	0.57 RPM
YRI_NA19214	0.32 RPM
YRI_NA19223	0.60 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).