RetrogeneDB ID: retro_hsap_3925

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:214256..214661(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000254104
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNF11
• Ensembl ID: ENSG00000123091
• Aliases: RNF11, SID1669
• Description: ring finger protein 11 [Source:HGNC Symbol;Acc:10056]

Sequence

>retro_hsap_3925
CTGAGACGCCCCACCTCAGATGACACTATTGTGCAACCGTCGACAGGGCAGGATCTTAGGCCCCTACTGCCACATATGGA
ACAAGCTCCAGTTCCAGTCTATCACCCAGCACCTGGCCAGCCTCTGTTAGCAATACTGCTGACTGAAGAAGAACAAGTTA
GAACAGCTCAAAGACTAAGCCTTCTACAGTGTCTGCCTGAAGAAGTTTATGACCCTGGAAGAGATAAATCAGAAGAGGAG
ATGCCAGAGTGTGTGATCTGTTTACTGGAATTTGTTTGTGGGGACCCCATTCGATGTCTGCCATGCAAACACTTCTTTCA
CCTTGACTGCATAGACACATGGCTGCTGCGATCTTTCACATGTCCCTACTGCCGGGGGCCAGTGGATGCAGCGCTGTCTA
CATCC

Alignment

ORF - retro_hsap_3925 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 87.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LHESQSDRASFGEGTEPDQEPPPPYQEQVPVPVYHPTPSQTRLATQLTEEEQIRIAQRIGLIQHLPKGVY
          L....SD.......T..D..P..P..EQ.PVPVYHP.P.Q..LA..LTEEEQ.R.AQR..L.Q.LP..VY
Retrocopy LRRPTSDDTIVQPSTGQDLRPLLPHMEQAPVPVYHPAPGQPLLAILLTEEEQVRTAQRLSLLQCLPEEVY

Parental  DPGRDGSEKKIRECVICMMDFVYGDPIRFLPCMHIYHLDCIDDWLMRSFTCPSCMEPVDAALLSS
          DPGRD.SE....ECVIC...FV.GDPIR.LPC.H..HLDCID.WL.RSFTCP.C..PVDAAL..S
Retrocopy DPGRDKSEEEMPECVICLLEFVCGDPIRCLPCKHFFHLDCIDTWLLRSFTCPYCRGPVDAALSTS

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	0.04 RPM	182.90 RPM
bodymap2_adrenal	0.00 RPM	121.69 RPM
bodymap2_brain	0.00 RPM	384.77 RPM
bodymap2_breast	0.02 RPM	294.19 RPM
bodymap2_colon	0.00 RPM	250.19 RPM
bodymap2_heart	0.00 RPM	141.69 RPM
bodymap2_kidney	0.00 RPM	201.53 RPM
bodymap2_liver	0.00 RPM	76.83 RPM
bodymap2_lung	0.00 RPM	261.69 RPM
bodymap2_lymph_node	0.00 RPM	112.82 RPM
bodymap2_ovary	0.00 RPM	269.32 RPM
bodymap2_prostate	0.03 RPM	209.64 RPM
bodymap2_skeletal_muscle	0.00 RPM	121.00 RPM
bodymap2_testis	0.08 RPM	185.89 RPM
bodymap2_thyroid	0.09 RPM	216.60 RPM
bodymap2_white_blood_cells	0.00 RPM	175.60 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3925 was not detected

EST

No EST(s) were mapped for retro_hsap_3925 retrocopy.

TSS

No TSS is located nearby retro_hsap_3925 retrocopy 5' end.

Lab

retro_hsap_3925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3925 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000006072	1 retrocopy	retro_etel_873,
Homo sapiens	ENSG00000123091	1 retrocopy	retro_hsap_3925 ,
Gorilla gorilla	ENSGGOG00000004919	1 retrocopy	retro_ggor_2641,
Myotis lucifugus	ENSMLUG00000004439	1 retrocopy	retro_mluc_145,
Otolemur garnettii	ENSOGAG00000011682	1 retrocopy	retro_ogar_2003,
Pongo abelii	ENSPPYG00000001361	1 retrocopy	retro_pabe_3241,
Pan troglodytes	ENSPTRG00000041089	1 retrocopy	retro_ptro_2669,
Ictidomys tridecemlineatus	ENSSTOG00000020072	4 retrocopies	retro_itri_1747, retro_itri_1886, retro_itri_633, retro_itri_974,
Tursiops truncatus	ENSTTRG00000010211	1 retrocopy	retro_ttru_1644,