RetrogeneDB ID: retro_ptro_1245

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:2098492..2099359(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TERF1
• Ensembl ID: ENSPTRG00000022919
• Aliases: None
• Description: None

Sequence

>retro_ptro_1245
GCGGATGGTAGGGATGCCAACCCTACCGAGGAGCAGATGGCAGAAACAGAGAGAAACGATGAGGAGCAGTTCAAATGCCA
GGAACGGCTCAAGTGCCAGGTGCAGGTGGGGGCCCCCGAGGAGGAGGAGGAGGACGCGGGCCTGGTGGCCTAGGCTGAGG
CCATGGCTGCTGGCTGGATGCTCGATTTCCTCTGCCTCTCTCTTTGCCGAGCTTTCCGCGACGGCCGCTCCAAGGACTTC
TGCAGGACCCGCAACAGCGCAGAGGCTATTATTCACGGACTATCCACTCTAACAGCTTACCAGTTGAGAATGATATATAT
ATGTCAGTTTTTGACAAGAATTGCAGCAGGAAAAACCCTTGATGCACAGTTTGAAAATGATGAACGAATTATACCCTTGG
AATCAGCCCTGATGATTTGGGGTTCAATTGAAAAGGAACATGACAAACTTCAAGAAGAAATACAGACTGAAATTCAGGCT
ATAGCTGTTTGTATGGAAAATGGCAACTTTAAAGAAGCAGAAGTCTTTGAAAGAATATTTGGTGATCCAAATTCTTATAT
GCCTCTCAAAAGCAAATTGCTTGTGATAATCTCTCAGAAAGATACATTTCATTCCTTTTTTTCAACACTTCAGCTACAAC
CACATGATGGAGAAAATTAAGAGTTATGTGAATTATGTGCTAAGTGAAAAATCATCAACCTTTCTAATGAAGGCAGCAGC
AAAAGTAGTAGAAAGTAAAAGAACAAGAACAATAACTTCTCAAGATAAACCTAATGGTAATTATGTTGAAATGGAAACTG
AAGCTAATTTGATACAAGAAAAAGGTCTCACAAGAATCTTTTCTTATCTAAGTTGCAACATGGAACT

Alignment

ORF - retro_ptro_1245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.58 %
• Parental protein coverage: 67.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ADGRDADPTEKQMAETERNDEEQFECQELLECQVQVGAPDEEEEEEEDAGLVAEAEAVAAGWMLDFLCLS
          ADGRDA.PTE.QMAETERNDEEQF.CQE.L.CQVQVGAP...EEEEEDAGLVA.AEA.AAGWMLDFLCLS
Retrocopy ADGRDANPTEEQMAETERNDEEQFKCQERLKCQVQVGAP---EEEEEDAGLVA*AEAMAAGWMLDFLCLS

Parental  LCRAFRDGRSEDFRRTRNSAEAIIHGLSSLTAYQLRTIYICQFLTRIAAGKTLDAQFENDERITPLESAL
          LCRAFRDGRS.DF.RTRNSAEAIIHGLS.LTAYQLR.IYICQFLTRIAAGKTLDAQFENDERI.PLESAL
Retrocopy LCRAFRDGRSKDFCRTRNSAEAIIHGLSTLTAYQLRMIYICQFLTRIAAGKTLDAQFENDERIIPLESAL

Parental  MIWGSIEKEHDKLHEEIQNLIKIQAIAVCMENGNFKEAEEVFERIFGDPNSHMPFKSKLLMIISQKDTFH
          MIWGSIEKEHDKL.EEIQ....IQAIAVCMENGNFKEA.EVFERIFGDPNS.MP.KSKLL.IISQKDTFH
Retrocopy MIWGSIEKEHDKLQEEIQT--EIQAIAVCMENGNFKEA-EVFERIFGDPNSYMPLKSKLLVIISQKDTFH

Parental  S-FFQHFSYNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVVESKRTRTITSQDKPSGNDVEMETEANL-DT
          S.FFQHFSYNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVVESKRTRTITSQDKP.GN.VEMETEANL.DT
Retrocopy S>FFQHFSYNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVVESKRTRTITSQDKPNGNYVEMETEANL<DT

Parental  RKSVSDKQSAVTESSEGT
          RK..S.K.........GT
Retrocopy RKR-SHKNLFLSKLQHGT

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	15.26 RPM
SRP007412_cerebellum	0.00 RPM	16.53 RPM
SRP007412_heart	0.00 RPM	7.87 RPM
SRP007412_kidney	0.00 RPM	12.08 RPM
SRP007412_liver	0.00 RPM	5.79 RPM
SRP007412_testis	0.00 RPM	14.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1245 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1245 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1245 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2493
Homo sapiens	retro_hsap_4324
Pan troglodytes	retro_ptro_802
Pan troglodytes	retro_ptro_1445

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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,