RetrogeneDB ID: retro_ptro_3074

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL393527.1:208935..209724(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040021
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FBL
• Ensembl ID: ENSPTRG00000010982
• Aliases: None
• Description: None

Sequence

>retro_ptro_3074
AGAGGTGGTGGAGGCTTCCATTCTGGTGGCAACCGGGGTCGTGGTCGGGGAGGAAAAAGAGGAAACCAGTCGGGGAAGAA
TGTGATGGTGGAGCCACATCGGCATGAGGGTGTCTTCATTTGTCGAGGAAAGGAAGATGCACTGGTCACCAAGAACCTGG
TCCCTGGGGAATCAGTTTATGGAGAGAAGAGAGTCTTGATTTCGGAAGGAGATGACAAAATTGAGTACCGAGCCTGGAAC
CCCTTCCGCTCCAAGCTAGCAGCAGCAATCCTGGGTGGTGTGGACCAGATCCACATCAAACCGGGGGCTAAGGTTCTCTA
CCTCGGGGCTGCCTCGGGCACCACGGTCTCCCATGTCTCTGACATCGTTGGTCCGGATGGTCTAGTCTATGCAGTCGAGT
TCTCCCACCGCTCTGGCCGTGACCTCATTAACTTGGCCAAGAAGAGGACCAACATCATTCCTGTGATCGAGGATGCTCAA
CACCCACACAAATACCGCATGCTCATCGCAATGGTGGATGTGATCTTTGCTGATGTGGCCCAGCCAGACCAGACCCGGAT
TGTGGCCCTGAATGCCCACACCTTCCTGCGTAATGGAGGACACTTTGTGATTTCCATTAAGGCCAACTCCATTGACTCCA
CAGCCTCAGCCGAGGCCGTGTTTGCCTCCGAAGTGAAAAAGATGCAACAGGAGAACATGAAGCCGCAGGAGCAGTTGACC
CTTTAGCCATACGAAAGAGACCATGCCGTGGTCGTGGGAGTGTACAGGCCACCCCCCAAGGTGAGGAAC

Alignment

ORF - retro_ptro_3074 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.1 %
• Parental protein coverage: 81.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGGGGFHSGGNRGRGRGGKRGNQSGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSISEG
          RGGGGFHSGGNRGRGRGGKRGNQSGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRV.ISEG
Retrocopy RGGGGFHSGGNRGRGRGGKRGNQSGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVLISEG

Parental  DDKIEYRAWNPFRSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGR
          DDKIEYRAWNPFRSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGR
Retrocopy DDKIEYRAWNPFRSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGR

Parental  DLINLAKKRTNIIPVIEDARHPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANC
          DLINLAKKRTNIIPVIEDA.HPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKAN.
Retrocopy DLINLAKKRTNIIPVIEDAQHPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANS

Parental  IDSTASAEAVFASEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPPKVKN
          IDSTASAEAVFASEVKKMQQENMKPQEQLTL.PYERDHAVVVGVYRPPPKV.N
Retrocopy IDSTASAEAVFASEVKKMQQENMKPQEQLTL*PYERDHAVVVGVYRPPPKVRN

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	10.80 RPM	23.33 RPM
SRP007412_cerebellum	6.35 RPM	44.92 RPM
SRP007412_heart	2.54 RPM	26.44 RPM
SRP007412_kidney	8.39 RPM	42.29 RPM
SRP007412_liver	5.79 RPM	61.87 RPM
SRP007412_testis	4.43 RPM	49.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3074 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3074 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3074 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002579	1 retrocopy	retro_btau_108,
Canis familiaris	ENSCAFG00000005412	1 retrocopy	retro_cfam_1697,
Homo sapiens	ENSG00000105202	1 retrocopy	retro_hsap_99,
Macropus eugenii	ENSMEUG00000014684	1 retrocopy	retro_meug_1077,
Microcebus murinus	ENSMICG00000007686	1 retrocopy	retro_mmur_1127,
Mus musculus	ENSMUSG00000046865	4 retrocopies	retro_mmus_1141, retro_mmus_1585, retro_mmus_1609, retro_mmus_89,
Nomascus leucogenys	ENSNLEG00000014234	1 retrocopy	retro_nleu_1947,
Otolemur garnettii	ENSOGAG00000006463	2 retrocopies	retro_ogar_3102, retro_ogar_504,
Pan troglodytes	ENSPTRG00000010982	2 retrocopies	retro_ptro_2208, retro_ptro_3074 ,
Pteropus vampyrus	ENSPVAG00000010849	1 retrocopy	retro_pvam_231,
Rattus norvegicus	ENSRNOG00000019229	4 retrocopies	retro_rnor_1082, retro_rnor_1780, retro_rnor_643, retro_rnor_75,
Sus scrofa	ENSSSCG00000030510	1 retrocopy	retro_sscr_39,
Tupaia belangeri	ENSTBEG00000007755	2 retrocopies	retro_tbel_3774, retro_tbel_3974,