RetrogeneDB ID: retro_ptro_2095

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:139044829..139045690(-)
• 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_2095
GCCCCGAGCCCGCGGAGTTGTGCGGCTGGTAGGGATGCCGACCCTACCGAGGAGCAGATGGCAGAAACAGAGAGCAACGA
CGAGGAGCAGTTCGAGTGCCAGGAACTGCTCGAGTGCCAGGTGCAGGTGGGGGCGGGCAAGGAGGAGGAGGAGGACGCCG
GCCTGGTGGCCGAGGCCAAGGCCATGGCTGCCGGCTGGATGCTCGATTTCCTCCGCCTCTCTCTTTGCGGAGCTTTCCGC
GAGGGCCGCTCCGAGGACTTCCGCGGGACCCGCAACAGCGCAGAGGCTATTATTCATGGACTATCCAGTCTAACAGCTTA
CCAGTTGAGAACAATATACATATGTCAGTTTTTGACAAGAATTGCAGCAGGAAAAACCCTTGATGCACAGTTCGAAAATG
ATGAACGAATTACACCCTTGGAATCAGCCCTGATGATTTGGGGTTCAATTGAAAAGGAACATGACCAACTTCACGAAGAA
ATACAGAATTTAATTAAAATTCAGGCTACAGCTGTTTGTATGGAAAATGGCAACTTTAAAGAAGCAGAAGAAGTCTTTGA
AAGAATATTTGGTGATCCAAATTTTCATATGCCTCTCAAAAGCAAATTGCTTATGATAATCTCTCAGAAAGATACATTTC
ATTCCTTTTTTCAACACTTCAGGTACAACCACATGAGGGAGAAAATTAAGAATTATGTGAATTATGTGTTAAGTGAAAAA
TCATCAACCTTTCTAATGAAGGCAGCAGCAAAAGTAGTAGAAAGTAAAAGAACAAGCACAGTCACTTCTCAAGATAAACC
TAATGGTAATGATGCTGAAATGGAAACTGAAGCTAATTTGGATACAAGAAAAAGTCTCACA

Alignment

ORF - retro_ptro_2095 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.17 %
• Parental protein coverage: 66.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APSPRGCADGRDADPTEKQMAETERNDEEQFECQELLECQVQVGAPDEEEEEEEDAGLVAEAEAVAAGWM
          APSPR.CA.GRDADPTE.QMAETE.ND...............VGA.....EEEEDAGLVAEA.A.AAGWM
Retrocopy APSPRSCAAGRDADPTEEQMAETESNDXXXXXXXXXXXXXXXVGAG---KEEEEDAGLVAEAKAMAAGWM

Parental  LDFLCLSLCRAFRDGRSEDFRRTRNSAEAIIHGLSSLTAYQLRTIYICQFLTRIAAGKTLDAQFENDERI
          LDFL.LSLC.AFR.GRSEDFR.TRNSAEAIIHGLSSLTAYQLRTIYICQFLTRIAAGKTLDAQFENDERI
Retrocopy LDFLRLSLCGAFREGRSEDFRGTRNSAEAIIHGLSSLTAYQLRTIYICQFLTRIAAGKTLDAQFENDERI

Parental  TPLESALMIWGSIEKEHDKLHEEIQNLIKIQAIAVCMENGNFKEAEEVFERIFGDPNSHMPFKSKLLMII
          TPLESALMIWGSIEKEHD.LHEEIQNLIKIQA.AVCMENGNFKEAEEVFERIFGDPN.HMP.KSKLLMII
Retrocopy TPLESALMIWGSIEKEHDQLHEEIQNLIKIQATAVCMENGNFKEAEEVFERIFGDPNFHMPLKSKLLMII

Parental  SQKDTFHSFFQHFSYNHMMEKIKSYVNYVLSEKSSTFLMKAAAKVVESKRTRTITSQDKPSGNDVEMETE
          SQKDTFHSFFQHF.YNHM.EKIK.YVNYVLSEKSSTFLMKAAAKVVESKRT.T.TSQDKP.GND.EMETE
Retrocopy SQKDTFHSFFQHFRYNHMREKIKNYVNYVLSEKSSTFLMKAAAKVVESKRTSTVTSQDKPNGNDAEMETE

Parental  ANLDTRKSVS
          ANLDTRKS..
Retrocopy ANLDTRKSLT

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	0.04 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_2095 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2095 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2095 has 0 orthologous retrocopies within eutheria group .

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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,