RetrogeneDB ID: retro_ptro_3241

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:83686741..83687503(-)
• 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_3241
TGTATGGAAAATGGCAACTTTAAAGAAGCAGAAGAAGTCTTTGAAAGAATATTTGGTGATCCAAATTCTTATATGCCTTT
GAAAAGCAAATTGCTTATGATAATCTCTCAGAAAGATACATTTCATTCCTTTTTTCAACACTTCAGCTACAACCACATGA
TGGAGAAAATTAAGAGTTACGTGAATTATGTGCTAAGTGAAAAATCATCAACCTTTCTAATGAAGGCAGTGGAAAAAGTA
GTAGAAAGCAAAAGGACAAGAACAATAACTTCTCAAGATAAACCTAATGGTAATGATGTTGAAATGGAAACTGAAGCTAA
TTTGGATACAAGAAAAATTGTTAGTGACAAACAGTCTGCGGTAACTGAATCCTCAGAGGGTACAGTATCCTTATTGAGGT
CTCACAAGAATCTTTTCTTATCTAAGATGCAACATGGAGCCGAGCAACAAGACCTTAATAAGAAAGAAAGAATAGGAATT
CTTCAAAGTACAAAAAAGAATAAAGAAAGCAGAAAAGCCACTGAAAGCAGAATACCTGTTTCAAAGAGTCAACCGGTAAC
TCCTGAAAAACATCGAGCTAGAAAAAGACAGGCATGGCTTTGGGAAGAAGACAAGAATTTGAGATCTGGCATGAGGAAAT
ATGGAGAGGGAAACTGGTCTAAAATACTGTTGCATTATAAATTCAACAACCGGACAAGTGTCATGTTAAAAGACAGATGG
AGGACCATGAAGAAAGTAAAACTGATTTGCTCGGACAGCAAA

Alignment

ORF - retro_ptro_3241 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.55 %
• Parental protein coverage: 58.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CMENGNFKEAEEVFERIFGDPNSHMPFKSKLLMIISQKDTFHSFFQHFSYNHMMEKIKSYVNYVLSEKSS
          CMENGNFKEAEEVFERIFGDPNS.MP.KSKLLMIISQKDTFHSFFQHFSYNHMMEKIKSYVNYVLSEKSS
Retrocopy CMENGNFKEAEEVFERIFGDPNSYMPLKSKLLMIISQKDTFHSFFQHFSYNHMMEKIKSYVNYVLSEKSS

Parental  TFLMKAAAKVVESKRTRTITSQDKPSGNDVEMETEANLDTRKSVSDKQSAVTESSEGTVSLLRSHKNLFF
          TFLMKA..KVVESKRTRTITSQDKP.GNDVEMETEANLDTRK.VSDKQSAVTESSEGTVSLLRSHKNLF.
Retrocopy TFLMKAVEKVVESKRTRTITSQDKPNGNDVEMETEANLDTRKIVSDKQSAVTESSEGTVSLLRSHKNLFL

Parental  SKLQHGTQQQDLTKKERRVGTLQSTKKKKESRRATESRIPVSKSQPVTPEKHRARKRQAWLWEEDKNLRS
          SK.QHG..QQDL.KKE.R.G.LQSTKK.KESR.ATESRIPVSKSQPVTPEKHRARKRQAWLWEEDKNLRS
Retrocopy SKMQHGAEQQDLNKKE-RIGILQSTKKNKESRKATESRIPVSKSQPVTPEKHRARKRQAWLWEEDKNLRS

Parental  GVRKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKKLKLICSDSE
          G.RKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKK.KLICSDS.
Retrocopy GMRKYGEGNWSKILLHYKFNNRTSVMLKDRWRTMKKVKLICSDSK

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	0.03 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_3241 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3241 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3241 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,