RetrogeneDB ID: retro_ptro_705

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:76034611..76035646(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RTN4IP1
• Ensembl ID: ENSPTRG00000018461
• Aliases: None
• Description: None

Sequence

>retro_ptro_705
ATGGAATTTCTGAAGACTTGTGTACTTAGAAGAAATGCGTGTACTGTGGTTTGCTTCTGGAGAAGCAAAGTTGTCCAAAG
GCCTTCCATTAGAAGGATTAGTACTACCTCTCCAAGGAGCACTGTCATGCCTGCTTGGGTGATAGATAAGTATGGGAAGA
ATGAAGTGCTTCGATTGACTCAGAACGTGATGATACCTATCATACGATATCCAAATGAAGTCATTGTAAAAGTTCACCCT
GCCAGTGTAAATCCTATAGACGTCAATATGAGAAGTGGTTATGGAGCTACAGCTTTAAATATGAAGCGTAATCCTTTACA
CATGAAAATCAAAGGAGAAGAATTTCCTCTGACTCTGATTCGGGATGTCTCTGGCATGGTGATGGAATGTGGGCTGGATG
TGAAGTACTTCAAGCCTTGAGATAAGGTCTGGGCTGCAGTTCCTCCTTGGAAACAAGGCACTCTTTCAGAGTTTGTTGTA
GTCAGTGGAAATGAGGTCTCTCACAAACCCAAATCACTCACTCATATATCAAGCTGCCTCTTCGCCATATGTGGCTCTCA
CAGCCTCATCTGCCATAAACAAAGTTGGTGACCTGAATGACAAGAATTGCACAGGAAGACATGTTCTAATCTTAGGCGCT
TCAGGCGGAGTTGGTGTTTTGCTATACAGGTAATGAAAGCATGGGATGCTCATGTGACAGCAGTTTGCGCTCAAGATGCC
AGTGAGCTTATAAAGAAGCTTGGGGCAGATGATGTAATTGATCACAAATTTGGAAGTGTGGAAGAGCAGTTGAAATCCTT
AAAACCGTTTGATTTCATCCTTGGTAATGTTGGCGGATCCACTAAAACATGGGCTCCAGATTTTCTCAAGAAATGGTCAG
GAGCCACCTATGTGACTTTGGTGAGTCCTTTCCTCCTGAACATGGACTGATTGGGCATAGCAGATGGCATGTTGCAGGCA
GGAGTCACCATAGGTTCGAAGGCATTAAAGCATTTCTGGAAAGGAGTCCATTATCGCTGGGCGTTTTTCATGGCC

Alignment

ORF - retro_ptro_705 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.91 %
• Parental protein coverage: 87.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEFLKTCVLRRNACTAVCFWRSKVVQKPSVRRISTTSPRSTVMPAWVIDKYGKNEVLRFTQNMMMPIIHY
          MEFLKTCVLRRNACT.VCFWRSKVVQ.PS.RRISTTSPRSTVMPAWVIDKYGKNEVLR.TQN.M.PII.Y
Retrocopy MEFLKTCVLRRNACTVVCFWRSKVVQRPSIRRISTTSPRSTVMPAWVIDKYGKNEVLRLTQNVMIPIIRY

Parental  PNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHMKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPG
          PNEVIVKVH.ASVNPIDVNMRSGYGATALNMKR.PLHMKIKGEEFPLTL.RDVSG.VMECGLDVKYFKP.
Retrocopy PNEVIVKVHPASVNPIDVNMRSGYGATALNMKRNPLHMKIKGEEFPLTLIRDVSGMVMECGLDVKYFKP*

Parental  DEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHT-QAASLPYVALTAWSAINKVGGLNDKNCTGKRVL
          D.VWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTH..QAAS.PYVALTA.SAINKVG.LNDKNCTG..VL
Retrocopy DKVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHI>QAASSPYVALTASSAINKVGDLNDKNCTGRHVL

Parental  ILGASGGVGT-FAVQVMKAWDAHVTAVCSQDASELVRKLGADDVIDYKSGSVEEQLKCLKPFDFILDNVG
          ILGASGGVG..FA.QVMKAWDAHVTAVC.QDASEL..KLGADDVID.K.GSVEEQLK.LKPFDFIL.NVG
Retrocopy ILGASGGVGV<FAIQVMKAWDAHVTAVCAQDASELIKKLGADDVIDHKFGSVEEQLKSLKPFDFILGNVG

Parental  GSTETWAPDFLKKWSGATYVTLVTPFLLNMDRLGIADGMLQTGVTVGSKALKHFWKGVHYRWAFFMA
          GST.TWAPDFLKKWSGATYVTLV.PFLLNMD.LGIADGMLQ.GVT.GSKALKHFWKGVHYRWAFFMA
Retrocopy GSTKTWAPDFLKKWSGATYVTLVSPFLLNMD*LGIADGMLQAGVTIGSKALKHFWKGVHYRWAFFMA

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	5.92 RPM
SRP007412_cerebellum	0.00 RPM	8.14 RPM
SRP007412_heart	0.00 RPM	7.08 RPM
SRP007412_kidney	0.03 RPM	7.51 RPM
SRP007412_liver	0.00 RPM	3.18 RPM
SRP007412_testis	0.00 RPM	8.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_705 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_705 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_705 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1030
Gorilla gorilla	retro_ggor_814
Pongo abelii	retro_pabe_863

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130347	1 retrocopy	retro_hsap_1030,
Gorilla gorilla	ENSGGOG00000008254	1 retrocopy	retro_ggor_814,
Nomascus leucogenys	ENSNLEG00000013349	1 retrocopy	retro_nleu_908,
Otolemur garnettii	ENSOGAG00000012703	1 retrocopy	retro_ogar_590,
Pongo abelii	ENSPPYG00000016882	1 retrocopy	retro_pabe_863,
Pan troglodytes	ENSPTRG00000018461	1 retrocopy	retro_ptro_705 ,