RetrogeneDB ID: retro_hsap_3881

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:98596158..98597551(-)
• Located in intron of: ENSG00000196367

Retrocopy information

• Ensembl ID: ENSG00000238109
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNF14
• Ensembl ID: ENSG00000013561
• Aliases: RNF14, ARA54, HFB30, TRIAD2
• Description: ring finger protein 14 [Source:HGNC Symbol;Acc:10058]

Sequence

>retro_hsap_3881
ATGTTGTCAGAAGACTGAGAAGCTCAGGAGGTGAGCTGCTGGCCCTGGCGAGTATTTAAGATGGAGATGAATTCGGAAAA
GCAAAGCCTGTCTGAGGTGGAGAAATCAGCATCGATCGGGATTTGCCACAGAACTTCAAGTTATTTGTGAGCGGCAATTC
AGATGAGTGCCCCCAGAATAGTAGCTTTGAATATACCATTTGCTTTCTCCCTCCACTTGTGCTGAACTCTGAACTGCCAC
CAGATTATCCATCCTCCTTCCCACCTTCATTCACACTTAGTGGCAAATTGCTGTCACCAACTCAGCTCTCTGCTCTATGC
AAGCACTTAGACAACCTATGGGAAGAACACAGTGGCAGTGGGATCCTGTCTGCCTGGATGCAGTTTCTTAAGCAAGAGAC
CCTGGTGCACCCCAATATTGTCTCTCCCTCTGAGCTCACGATAAGTTCTCAGGAAAAAGTGCCGAGAAGGATAGCTCAAG
CCCCTCCCATCAGAGCTAGATTTTGGAGGAGCTGCTGGATCTCATGTAGATCAAGAGGAAATTGTGGATGAGAGAGCTGT
GCAGGATGTGGAATCACTGTCAAGTCTGATCCAGGAAATCTTGGACTTTGATCAAGCTTAGCAGATAAAATGCTTTAATA
GTAGACTGTTCCTGTACGACATCTGTTTCTGCGAGAAGCTGGGCAGTGAATGCATGTACTTCTTGGAGTGAAGCCTGTGT
ACTGCAAAGCCTATCTGAAGGACTGCTTTGAAATCCAGATCAGAGATGGCCAGGTTCAATGCCTCAACTGCTCAGAACCA
AAGTGCCCTTCGGTGGCCACTCCTGGCCAGGTCAAAGAGCCAGCGGAAGCAGAGTTCTCTGCCCGTCATGGCTGCCTTCT
CCTCCCATCCACCTTGGAGCTGGTGGCAGATGTGGTGTGCTGCCCCCGCCTGTGGGGGCCTGCAGGGCCTGGCTGTACCA
CGGGCATCTGCTCCAGCTGTAACTTTGCCTTCTGTACCTTGTGCAGACTGACCTACCATGGGGCCTCTCCATGTAAGGTG
ATGGCAGAGAAATTAACAGACTTACAAAACGAATACCTGCAAGCAGATGAGGCCAAGACAAGATTTCTGTAACAGAGGTA
AGGTAAGAGGGTGAGTCAGAGGGCACTGGAAGAGATGGAAAGAAAGGAGTGGCTAGAAGAGAACTCGAAGAGATGCCCAT
GCTGTGGAATTCACATAGAGAAGTGAGGTGGATGCCATGTACTGGCTGCAGGCTCTATTTCTATTGGGTCGGCATGGGTT
CTCTCTCTAGCAACCCCTTACAAACATTTCGCCAACCCTACTTCACCGTGTTGTAACCGGCTGTTTCATGCTTGGATATG
AATGGAGACATTGGGGAAGATGAGATTGAAGAC

Alignment

ORF - retro_hsap_3881 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 8
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSSEDREAQE-DELLALASIYDGDEFRKAESVQGGETRIYLDLPQNFKIFVSGNSNECLQNSGFEYTICF
          M.SED.EAQE..ELLALASI.DGDEF.KA..V.GGE..I..DLPQNFK.FVSGNS.EC.QNS.FEYTICF
Retrocopy MLSED*EAQE<GELLALASI*DGDEFGKAKPV*GGEISIDRDLPQNFKLFVSGNSDECPQNSSFEYTICF

Parental  LPPLVLNFELPPDYPSSSPPSFTLSGKWLSPTQLSALCKHLDNLWEEHRGSVVLFAWMQFLKEETLAYLN
          LPPLVLN.ELPPDYPSS.PPSFTLSGK.LSPTQLSALCKHLDNLWEEH.GS..L.AWMQFLK.ETL...N
Retrocopy LPPLVLNSELPPDYPSSFPPSFTLSGKLLSPTQLSALCKHLDNLWEEHSGSGILSAWMQFLKQETLVHPN

Parental  IVSPFELKIGSQ-KKVQRRTAQASPNTELDFGGAAGSDVDQEEIVDERAVQDVESLSNLIQEILDFDQAQ
          IVSP.EL.I.SQ.KK.........P..ELDFGGAAGS.VDQEEIVDERAVQDVESLS.LIQEILDFDQA.
Retrocopy IVSPSELTISSQ>KKCREG*LKPLPS-ELDFGGAAGSHVDQEEIVDERAVQDVESLSSLIQEILDFDQA*

Parental  QIKCFNSKLFLCSICFCEKLGSECMYFLE-CRHVYCKACLKDYFEIQIRDGQVQCLNCPEPKCPSVATPG
          QIKCFNS.LFL..ICFCEKLGSECMYFLE....VYCKA.LKD.FEIQIRDGQVQCLNC.EPKCPSVATPG
Retrocopy QIKCFNSRLFLYDICFCEKLGSECMYFLE<VKPVYCKAYLKDCFEIQIRDGQVQCLNCSEPKCPSVATPG

Parental  QVKELVEAELFARYDRLLLQSSLDLMADVVYCPRPCCQLPVMQEPGCTMGICSSCNFAFCTLCRLTYHGV
          QVKE..EAE..AR...LLL.S.L.L.AD.V.C...C..L.....PGCT.GICSSCNFAFCTLCRLTYHG.
Retrocopy QVKEPAEAEFSARHGCLLLPSTLELVAD-VVC---CPRLWGPAGPGCTTGICSSCNFAFCTLCRLTYHGA

Parental  SPCKVTAEKLMDLRNEYLQADEANKRLLDQRYGKRVIQKALEEMESKEWLEKNSKSCPCCGTPIEKLDGC
          SPCKV.AEKL.DL.NEYLQADEA..R.L.QR.GKRV.Q.ALEEME.KEWLE.NSK.CPCCG..IEK..GC
Retrocopy SPCKVMAEKLTDLQNEYLQADEAKTRFL*QR*GKRVSQRALEEMERKEWLEENSKRCPCCGIHIEK*GGC

Parental  NKMTCTGCMQYFCWICMGSLSRANPYKHFNDPGSPCFNRLFYA-VDVDDDIWEDEVED
          .............W.....LS.A.PYKHF..P.SPC.NRLF.A..D...DI.EDE.ED
Retrocopy HVLAAGSISIGSAWV----LSLATPYKHFANPTSPCCNRLFHA<LDMNGDIGEDEIED

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	0.26 RPM	34.87 RPM
bodymap2_adrenal	0.74 RPM	33.53 RPM
bodymap2_brain	0.61 RPM	63.55 RPM
bodymap2_breast	0.39 RPM	89.16 RPM
bodymap2_colon	0.00 RPM	43.82 RPM
bodymap2_heart	0.00 RPM	94.50 RPM
bodymap2_kidney	0.08 RPM	91.01 RPM
bodymap2_liver	0.00 RPM	41.30 RPM
bodymap2_lung	0.00 RPM	28.73 RPM
bodymap2_lymph_node	0.00 RPM	34.83 RPM
bodymap2_ovary	0.33 RPM	49.52 RPM
bodymap2_prostate	0.00 RPM	58.91 RPM
bodymap2_skeletal_muscle	0.11 RPM	23.26 RPM
bodymap2_testis	0.11 RPM	85.91 RPM
bodymap2_thyroid	0.32 RPM	72.58 RPM
bodymap2_white_blood_cells	0.04 RPM	40.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3881 was not detected

EST

1 EST(s) were mapped to retro_hsap_3881 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA601332	98596145	98596583	100	438	0	438

TSS

No TSS is located nearby retro_hsap_3881 retrocopy 5' end.

Lab

retro_hsap_3881 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3881 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2643
Gorilla gorilla	retro_ggor_2612
Pongo abelii	retro_pabe_3115

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007803	1 retrocopy	retro_dnov_332,
Dasypus novemcinctus	ENSDNOG00000024423	1 retrocopy	retro_dnov_1704,
Homo sapiens	ENSG00000013561	2 retrocopies	retro_hsap_3790, retro_hsap_3881 ,
Gorilla gorilla	ENSGGOG00000008542	1 retrocopy	retro_ggor_2612,
Macaca mulatta	ENSMMUG00000009768	2 retrocopies	retro_mmul_1647, retro_mmul_934,
Pongo abelii	ENSPPYG00000015894	2 retrocopies	retro_pabe_3095, retro_pabe_3115,
Pan troglodytes	ENSPTRG00000017356	2 retrocopies	retro_ptro_2571, retro_ptro_2643,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.20 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.15 RPM
CEU_NA12760	0.18 RPM
CEU_NA12827	0.14 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.26 RPM
FIN_HG00183	0.25 RPM
FIN_HG00277	0.30 RPM
FIN_HG00315	0.11 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.07 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.18 RPM
GBR_HG00119	0.17 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.12 RPM
GBR_HG00134	0.11 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.17 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.31 RPM
TSI_NA20538	0.23 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.31 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.03 RPM
YRI_NA18916	0.11 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.13 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.10 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.10 RPM
YRI_NA19223	0.12 RPM

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Indel association:

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