RetrogeneDB ID: retro_hsap_4861

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:74546609..74547833(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000232186
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TERF1
• Ensembl ID: ENSG00000147601
• Aliases: TERF1, PIN2, TRBF1, TRF, TRF1, hTRF1-AS, t-TRF1
• Description: telomeric repeat binding factor (NIMA-interacting) 1 [Source:HGNC Symbol;Acc:11728]

Sequence

>retro_hsap_4861
GCCCCGAGCCCTTGGGGCTGTGCAGATGGTAGGGATGCCAACCCTACTGAGGAGCAGATGGCAGAAACAGAGAGAAACGA
CGAGGAGCAGTTCGAGTGCCAGGAACTGCTCGAGTGCTGGGTGCAGGTGGGAGCCCCCGAGGAGGAGGAGGAGGACCCGG
GCCTGGTGGCTGAGGCCGAGGCTGTGGCTGCTGGCTGGATGCTCGATTTCCTCTGCCTCTCTCTTTGCTGAGCTTTCCGC
GACGGCCGCCCTGAGGACTTCTGCCGGACCCGCAACAGCGCAGAGGCTATTATTCATGGACTATCCAGTCTAACAGCTTA
CCAGTTGAGAACAATATGCATATGTCAGTTTTTGACAAGCATTGCAGCAGGAAAAACCCTTGATGTACAGTTTGAAAATG
ATGAACGAATTACACCCTTGGAATCAGCCCTGATGATTTGGGGTTCAATTGAAAAGGAACATGACAAACTTCATGAAGAA
ATATAGAATTTAATTAAAATTCAGGCTATAGCTGTTTGTATGGAAAATGACAACTTTACAGAAGCAGAAGAAGTCTTTGA
AAGAATATTTGGTGATCCAAATTCTTATATGCCTCTCAAAAGCAAATTGCTTATGATAATCTCTCAGAAAGATACATTTC
ATTCCTTTTTTCAACACTTCAGCTACAATCACATGATGGAGAAAATTAAGAGTTATGTGAATTATGTGCTAAGTGAAAAA
TCATCAACCTTTCTAATGAAGGCAGCAGCAAAAGTAGTAGAAAGTAAAAGAACAAGAACAATAATTTCTCAAGATAAACC
TAATGGTAATGATGTTGAAATGGAAACTGAAGCTAATTTGGATACAAGAAAAAGGTCTCACAAGAATCTTTTCTTATCTA
AGTTGCAACATGGAACCCAGCAACAAGACCTTAATAAGAAAGAAAGGAGAGTAGGAACTCTTCAAAGTACAAAAAAGAAA
AAAGAAAGCAGAAGAGCCACTGAAAGCAGAATACCTATTTCAAAGAGTCAACTGGTAACTCCTGAAAAACATCAAGCTAA
AAAAAAACAAGCATGGCTTTGGGAAGAAGACAAGAATTTGAGATCTGGCGTGAGGAAACATGGAGAGGGAAACTGGTCTA
AAATACTATTGCATTATAAATTCAACAACCGGACAAGTGTCATATTAAAAGACAGATGGAGGACCATGAAGAAACTAAAA
CTGATTTGCTCAGACAGTGAAGAC

Alignment

ORF - retro_hsap_4861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.75 %
• Parental protein coverage: 98.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APSPRGCADGRDADPTEEQMAETERNDEEQFECQELLECQVQVGAPEEEEEEEEDAGLVAEAEAVAAGWM
          APSP.GCADGRDA.PTEEQMAETERNDEEQFECQELLEC.VQVGAP...EEEEED.GLVAEAEAVAAGWM
Retrocopy APSPWGCADGRDANPTEEQMAETERNDEEQFECQELLECWVQVGAP---EEEEEDPGLVAEAEAVAAGWM

Parental  LDFLCLSLCRAFRDGRSEDFRRTRNSAEAIIHGLSSLTACQLRTIYICQFLTRIAAGKTLDAQFENDERI
          LDFLCLSLC.AFRDGR.EDF.RTRNSAEAIIHGLSSLTA.QLRTI.ICQFLT.IAAGKTLD.QFENDERI
Retrocopy LDFLCLSLC*AFRDGRPEDFCRTRNSAEAIIHGLSSLTAYQLRTICICQFLTSIAAGKTLDVQFENDERI

Parental  TPLESALMIWGSIEKEHDKLHEEIQNLIKIQAIAVCMENGNFKEAEEVFERIFGDPNSHMPFKSKLLMII
          TPLESALMIWGSIEKEHDKLHEEI.NLIKIQAIAVCMEN.NF.EAEEVFERIFGDPNS.MP.KSKLLMII
Retrocopy TPLESALMIWGSIEKEHDKLHEEI*NLIKIQAIAVCMENDNFTEAEEVFERIFGDPNSYMPLKSKLLMII

Parental  SQKDTFHSFFQHFSYNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVVESKRTRTITSQDKPSGNDVEMETE
          SQKDTFHSFFQHFSYNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVVESKRTRTI.SQDKP.GNDVEMETE
Retrocopy SQKDTFHSFFQHFSYNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVVESKRTRTIISQDKPNGNDVEMETE

Parental  ANLDTRKRSHKNLFLSKLQHGTQQQDLNKKERRVGTPQSTKKKKESRRATESRIPVSKSQPVTPEKHRAR
          ANLDTRKRSHKNLFLSKLQHGTQQQDLNKKERRVGT.QS.......RRATESRIP.SKSQ.VTPEKH.A.
Retrocopy ANLDTRKRSHKNLFLSKLQHGTQQQDLNKKERRVGTLQSXXXXXXXRRATESRIPISKSQLVTPEKHQAX

Parental  KRQAWLWEEDKNLRSGVRKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKKLKLISSDSED
          ..QAWLWEEDKNLRSGVRK.GEGNWSKILLHYKFNNRTSV.LKDRWRTMKKLKLI.SDSED
Retrocopy XXQAWLWEEDKNLRSGVRKHGEGNWSKILLHYKFNNRTSVILKDRWRTMKKLKLICSDSED

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	0.52 RPM	22.20 RPM
bodymap2_adrenal	1.47 RPM	29.60 RPM
bodymap2_brain	0.96 RPM	36.24 RPM
bodymap2_breast	1.26 RPM	26.05 RPM
bodymap2_colon	0.17 RPM	31.38 RPM
bodymap2_heart	0.37 RPM	14.62 RPM
bodymap2_kidney	0.58 RPM	31.31 RPM
bodymap2_liver	0.15 RPM	13.39 RPM
bodymap2_lung	1.23 RPM	15.98 RPM
bodymap2_lymph_node	0.71 RPM	25.09 RPM
bodymap2_ovary	0.83 RPM	55.07 RPM
bodymap2_prostate	0.59 RPM	48.10 RPM
bodymap2_skeletal_muscle	0.38 RPM	5.37 RPM
bodymap2_testis	0.17 RPM	46.94 RPM
bodymap2_thyroid	0.38 RPM	34.72 RPM
bodymap2_white_blood_cells	0.18 RPM	31.56 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4861 was not detected

EST

No EST(s) were mapped for retro_hsap_4861 retrocopy.

TSS

No TSS is located nearby retro_hsap_4861 retrocopy 5' end.

Lab

retro_hsap_4861 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4861 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3236

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002407	1 retrocopy	retro_chof_944,
Callithrix jacchus	ENSCJAG00000007714	1 retrocopy	retro_cjac_1658,
Homo sapiens	ENSG00000147601	6 retrocopies	retro_hsap_1166, retro_hsap_1917, retro_hsap_2493, retro_hsap_3099, retro_hsap_4324, retro_hsap_4861 ,
Oryctolagus cuniculus	ENSOCUG00000002793	1 retrocopy	retro_ocun_546,
Pan troglodytes	ENSPTRG00000022919	7 retrocopies	retro_ptro_1245, retro_ptro_1445, retro_ptro_2095, retro_ptro_3236, retro_ptro_3241, retro_ptro_611, retro_ptro_802,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	1.07 RPM
CEU_NA11843	0.80 RPM
CEU_NA11930	0.52 RPM
CEU_NA12004	0.19 RPM
CEU_NA12400	0.70 RPM
CEU_NA12751	0.34 RPM
CEU_NA12760	0.76 RPM
CEU_NA12827	0.80 RPM
CEU_NA12872	0.54 RPM
CEU_NA12873	0.67 RPM
FIN_HG00183	1.87 RPM
FIN_HG00277	0.92 RPM
FIN_HG00315	0.61 RPM
FIN_HG00321	1.06 RPM
FIN_HG00328	0.54 RPM
FIN_HG00338	0.34 RPM
FIN_HG00349	0.34 RPM
FIN_HG00375	1.03 RPM
FIN_HG00377	0.43 RPM
FIN_HG00378	0.49 RPM
GBR_HG00099	0.26 RPM
GBR_HG00111	0.54 RPM
GBR_HG00114	0.60 RPM
GBR_HG00119	0.98 RPM
GBR_HG00131	1.24 RPM
GBR_HG00133	0.84 RPM
GBR_HG00134	0.81 RPM
GBR_HG00137	1.10 RPM
GBR_HG00142	1.36 RPM
GBR_HG00143	0.35 RPM
TSI_NA20512	0.28 RPM
TSI_NA20513	0.73 RPM
TSI_NA20518	0.56 RPM
TSI_NA20532	1.43 RPM
TSI_NA20538	0.55 RPM
TSI_NA20756	0.44 RPM
TSI_NA20765	0.89 RPM
TSI_NA20771	0.71 RPM
TSI_NA20786	0.10 RPM
TSI_NA20798	0.50 RPM
YRI_NA18870	0.68 RPM
YRI_NA18907	0.24 RPM
YRI_NA18916	0.42 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.37 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.41 RPM
YRI_NA19213	0.24 RPM
YRI_NA19214	0.15 RPM
YRI_NA19223	0.70 RPM

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Indel association:

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