RetrogeneDB ID: retro_ptro_802

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:18191705..18192545(+)
• 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_802
GCGGATGGTAGGGATGCCGACCCTACTGAGGAGCAGGTGGCAGAAACAGAGAGAAACGATGAGGAGCAGTTCGAATGCCA
GGAACGGCTCAAGTGCCAGGTGCAGGTGGGGGCCCCCGCGGAGGAGGAGGAGGAGGAGGAGGACGCGGGCCTGGTGGCCG
AGGCCGAGGCCGTGGCTGCCGGCTGCATGCTCGATTTCCTCTGCCTCTCTCTTTGCCGAGCTTTCCGCGACGGCCGCTCC
AAGGACTTCTGCAGGACCCGCAACAGCGCAGAGGCTATTATTCACGGACTATCCAGTCTAACAGCTTACCAGTTGAGAAT
GATATACGTATGTCAGTTTTTGACAAGAATTGCAGCAGGAAAAACCCTTGATGCACAGTTTGAAAATGATGAACGAATTA
CACCCTTGGAATCAGCCCTGATGATTTGGGGTTCGATTGAAAAGGAACATGACAAACTTCAAGAAGAAATACAGAATTTA
ATTAAAATTCAGGCTATAGCTGTTTGTATGGAAAATGACAACTTTAAAGAAGCAGAAGAAGTCTTTGAAAGAATATTTGG
TGATCCAAATTCTTACATGCCTCTCAAAAGCAAATTGCTTGTGATAATCTCTCAGAAAGATACATTTCATTCCTTTTTTC
AACACTTCAGCTACAACCACATGATGGAGAAAATTAAGAGTTATGTGAATTATGTGCTAAGTGAAAAATCATCAACCTTT
CTAATGAAGGCAGCAGCAAAAGTAGTAGAAAGTAAAAGAACAAGAACAATAACTTCTCAAGATAAACCTAATGGTAATTA
TGTTGACATGGAAACTGAAGCTAATTTGGATACAAGAAAA

Alignment

ORF - retro_ptro_802 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.71 %
• Parental protein coverage: 63.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADGRDADPTEKQMAETERNDEEQFECQELLECQVQVGAPDEEEEEEEDAGLVAEAEAVAAGWMLDFLCLS
          ADGRDADPTE.Q.AETERNDEEQFECQE.L.CQVQVGAP.........AGLVAEAEAVAAG.MLDFLCLS
Retrocopy ADGRDADPTEEQVAETERNDEEQFECQERLKCQVQVGAPXXXXXXXXXAGLVAEAEAVAAGCMLDFLCLS

Parental  LCRAFRDGRSEDFRRTRNSAEAIIHGLSSLTAYQLRTIYICQFLTRIAAGKTLDAQFENDERITPLESAL
          LCRAFRDGRS.DF.RTRNSAEAIIHGLSSLTAYQLR.IY.CQFLTRIAAGKTLDAQFENDERITPLESAL
Retrocopy LCRAFRDGRSKDFCRTRNSAEAIIHGLSSLTAYQLRMIYVCQFLTRIAAGKTLDAQFENDERITPLESAL

Parental  MIWGSIEKEHDKLHEEIQNLIKIQAIAVCMENGNFKEAEEVFERIFGDPNSHMPFKSKLLMIISQKDTFH
          MIWGSIEKEHDKL.EEIQNLIKIQAIAVCMEN.NFKEAEEVFERIFGDPNS.MP.KSKLL.IISQKDTFH
Retrocopy MIWGSIEKEHDKLQEEIQNLIKIQAIAVCMENDNFKEAEEVFERIFGDPNSYMPLKSKLLVIISQKDTFH

Parental  SFFQHFSYNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVVESKRTRTITSQDKPSGNDVEMETEANLDTRK
          SFFQHFSYNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVVESKRTRTITSQDKP.GN.V.METEANLDTRK
Retrocopy SFFQHFSYNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVVESKRTRTITSQDKPNGNYVDMETEANLDTRK

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_802 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_802 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_802 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2493
Homo sapiens	retro_hsap_4324
Pan troglodytes	retro_ptro_1245
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 ,