RetrogeneDB ID: retro_ptro_632

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:88849917..88851081(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSBPL9
• Ensembl ID: ENSPTRG00000000730
• Aliases: None
• Description: oxysterol binding protein-like 9 [Source:HGNC Symbol;Acc:16386]

Sequence

>retro_ptro_632
AAAACTTTAATTGTTCAATCAAGATTTGTAGGTAATTACATCAGCAGCAGCTCAGGAAATAGTCTAAAACATCCAGATAC
TAGAGAATCACTTAATTCTTCCATGTCCAATGGAACAAGTGATGCTGACCTTTTTGATTCATATGACAGTAGAGATGATG
ATGTGTAGGCGGAGTCCGCAGGGAGCACAAGAGCGTTATCATGCATCTGTTGTCACAGGTTAGGCTTGGGATGGATCTTA
CTAAGGTAGTTCTTCCAAGGTTTATTCTTGAAAGAAGATCTCTTTTAGAAATGTATGCAGACTTTTTGCACACTGGGACC
TGTTTGTGTCCATTAGTGACTAGAAGGATCACAAGGATAGAATGGTTCTGGTTGTGAAATCATACCTCTCAGCCTTTCAT
GCAAGAAGGAAAGGGCCAGTTGCCAAAGAGCCATACAATCCCATTTTGGGCAAGATTTTTCAGTGTCACTGGACACTACC
AAATGATACTGAAGAGAACACAAAACTAGTTTCAGAAAGACCAGTTCCCTGGGTTTCCAAAAATACTGTAACATTCGTGG
CTGACCAGGTTTCCCATCCTCAACCATTTCAGCCTTTTATGTTGAGTATTTTAACAAGAAGATACAATTCACTGCTCATG
TCTGGGCCAAATCAAAATTCCTTGGGATGTCAATTGGTGTTCACAACATAGGGCAGGGCTGTGTCTCATGTCTAGACTAT
GATGAACATTACATTCTCACATTCCTCAATGGCTATAGAAGGTCTATCCTCACATGGTCCTGGGTGAAATTAGGTGGAGA
ATGTTGTATTAATTGTTCCAAATAGGCTAGAGTGCAAATATCATCTTCCATACTAAACCCTTCTATGTGGGCAAGAAGCA
CAAAATTACTGCTGAGAATTTTCTCCAAATGACAAGAAGTCTTTTTGCTCAACTGAAGGGGAATGGAATGGTTTGATGTA
TGCAAAATATGCAACATGGGAAAATACATCCTTTGCAGATACCAAGAAGTTGCCTGTAATCAAGAAGAAAGTGATGAAGC
TAGAAGATCAGAACAAGTAAGAATCCAGCAGCCTTTGGAAGGATGTCACTTTCAACTTAAAAATCAGCAACTGAAGCAAA
GCACAGGCTTGAATAAAAGAGCAGAACCCCAAGTAAGGAAAGAG

Alignment

ORF - retro_ptro_632 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.79 %
• Parental protein coverage: 52.42 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KRLIDSSGSASVLTHSSSGNSLKRPDTTESLNSSLSNGTSDADLFDSHDDRDDDAEAGSV-EEHKSVIMH
          K.LI..S........SSSGNSLK.PDT.ESLNSS.SNGTSDADLFDS.D.RDDD..A.S...EHKSVIMH
Retrocopy KTLIVQSRFVGNYISSSSGNSLKHPDTRESLNSSMSNGTSDADLFDSYDSRDDDV*AESA<REHKSVIMH

Parental  LLSQVRLGMDLTKVVLPTFILERRSLLEMYADF-FAHPDLFVSISDQKDPKDRMVQVVKWYLSAFHAGRK
          LLSQVRLGMDLTKVVLP.FILERRSLLEMYADF.FAH.DLFVSISD.KD.KDRMV.VVK.YLSAFHA.RK
Retrocopy LLSQVRLGMDLTKVVLPRFILERRSLLEMYADF<FAHWDLFVSISD*KDHKDRMVLVVKSYLSAFHARRK

Parental  GSVAKKPYNPILGEIFQCHWTLPNDTEENTELVSEGPVPWVSKNSVTFVAEQVSHHPP-ISAFYAECFNK
          G.VAK.PYNPILG.IFQCHWTLPNDTEENT.LVSE.PVPWVSKN.VTFVA.QVSH..P.ISAFY.E.FNK
Retrocopy GPVAKEPYNPILGKIFQCHWTLPNDTEENTKLVSERPVPWVSKNTVTFVADQVSHPQP<ISAFYVEYFNK

Parental  KIQFNAHIWTKSKFLGMSIGVHNIGQGCVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSK-T
          KIQF.AH.W.KSKFLGMSIGVHNIGQGCVSCLDYDEHYILTF.NGY.RSILT..WV.LGGEC.INCSK..
Retrocopy KIQFTAHVWAKSKFLGMSIGVHNIGQGCVSCLDYDEHYILTFLNGYRRSILTWSWVKLGGECCINCSK<I

Parental  GYSANIIFHTKPFYGGKKHRITAE-IFSPNDKKSFCSIEGEWNGVMYAKYATGENTVFVDTKKLPIIKKK
          G.SANIIFHTKPFY.GKKH.ITAE..FSPNDKKSFCS.EGEWNG.MYAKYAT.ENT.F.DTKKLP.IKKK
Retrocopy G*SANIIFHTKPFYVGKKHKITAE<EFSPNDKKSFCSTEGEWNGLMYAKYATWENTSFADTKKLPVIKKK

Parental  VRKLEDQNEYESRSLWKDVTFNLKI-RDIDAATEAKHRLEERQRAE
          V.KLEDQN..ES.SLWKDVTFNLKI.......T....R.E...R.E
Retrocopy VMKLEDQNK*ESSSLWKDVTFNLKI<QQLKQSTGLNKRAEPQVRKE

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	21.38 RPM
SRP007412_cerebellum	0.00 RPM	35.24 RPM
SRP007412_heart	0.00 RPM	55.96 RPM
SRP007412_kidney	0.03 RPM	104.79 RPM
SRP007412_liver	0.00 RPM	60.17 RPM
SRP007412_testis	0.00 RPM	120.35 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_632 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_632 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_632 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021574	1 retrocopy	retro_cjac_1235,
Felis catus	ENSFCAG00000010298	1 retrocopy	retro_fcat_1134,
Gorilla gorilla	ENSGGOG00000004787	1 retrocopy	retro_ggor_737,
Microcebus murinus	ENSMICG00000002731	1 retrocopy	retro_mmur_1035,
Myotis lucifugus	ENSMLUG00000009199	1 retrocopy	retro_mluc_2149,
Nomascus leucogenys	ENSNLEG00000016138	2 retrocopies	retro_nleu_1820, retro_nleu_279,
Oryctolagus cuniculus	ENSOCUG00000004303	1 retrocopy	retro_ocun_281,
Pongo abelii	ENSPPYG00000001358	2 retrocopies	retro_pabe_689, retro_pabe_787,
Pan troglodytes	ENSPTRG00000000730	1 retrocopy	retro_ptro_632 ,
Ictidomys tridecemlineatus	ENSSTOG00000000692	1 retrocopy	retro_itri_1537,