RetrogeneDB ID: retro_ptro_1913

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:106751640..106752553(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSX2IP
• Ensembl ID: ENSPTRG00000000906
• Aliases: None
• Description: None

Sequence

>retro_ptro_1913
AGACAGTTACAATGCAAGAACAGGAATTTGAATCAGTTATTGAAAAATGAGAAGGATAAGGTACAGAAATTACAAAATAT
CATTGTAAGTTGAGCTATTCAGTATTATCATGATATGATATGAAAAGAGTGTGAATATAACAAACTGAAGGAAAGTCTAC
ATCAACCTTTTATGAACAAAAAAGAATTAAAAATAGCTTTAGACATTTTAAATAATGTGGGGAGAGCTGATGGAAAAAGA
GGCCTCTGGAAAACTGGTAAGACAGAAGTCAGGAATTTGATGAAATGTATAAAATTATCTTGAATGATTATGAGTATTGT
CACAAACAAGTCCTAATGGAAAATGCTGATAATGAAGAAGTGTGTTCATAAAGGGGACAAGGATATGTTTTTTTTCTTTC
TCCTCAAAAGAAACCTAGAGAAAGAGAAGATGGTAGTACAGGAACTGTCATCTCAGATGTTGAAGAAGATGCTGGGGAAA
TGAGCAGAGACAGTATCTGGGAACTTTCCTGTGAAACTGTGAGAGAACAGCCTACAAACAGCATCAGAAAACAGTGGGGA
ATTTTGAAAAGTCATGGAGAAAAACTTGGTAGCTATGTTTCAAAGGTACACTTAGAAAATTTAATGATGAAGATTTAATC
TCAAAACAAGACCATGAACAGGAAGCTGAAAAACTCAAATTAGAAATTCAGAAATGTAAAGAAATGATTAAAACTCAGCA
GCAACTTTTACAGCAACACCTCACTACTGGTTGTGATGATGATACCACTGCACTATTATGAGACTGTTATTTGGAAGAAA
AGGGATGCCACAAACGATGGCCCCTTTTTAAAGAGCAAAAAAATAATTTTCAGAGAGAAAGATGAAGCTTTATAGAAGCT
GCTATTCACCTAGGTTTGGAGAGGAAGGTGTTT

Alignment

ORF - retro_ptro_1913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.87 %
• Parental protein coverage: 50.16 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RQLQCKNRNLHQLLKNEKDEVQKLQNIIASRATQYNHDMKRKEREYNKLKERLHQLVMNKKDKKIAMDIL
          RQLQCKNRNL.QLLKNEKD.VQKLQNII.S.A.QY.HDM..KE.EYNKLKE.LHQ..MNKK..KIA.DIL
Retrocopy RQLQCKNRNLNQLLKNEKDKVQKLQNIIVS*AIQYYHDMI*KECEYNKLKESLHQPFMNKKELKIALDIL

Parental  NYVGRADGKRGSWRTGKTEARN-EDEMYKILLNDYEYRQKQILMENAELKKVLQQMKKEMISLLSPQKKK
          N.VGRADGKRG.W.TGKTE.RN..DEMYKI.LNDYEY..KQ.LMENA....V...........LSPQ.KK
Retrocopy NNVGRADGKRGLWKTGKTEVRN<FDEMYKIILNDYEYCHKQVLMENADNEEVCS*RGQGYXXXLSPQ-KK

Parental  PRERVDDSTGTVISDVEEDAGELSRESMWDLSCETVREQLTNSIRKQWRILKSHVEKLDNQVSKVHLEG-
          PRER.D.STGTVISDVEEDAGE.SR.S.W.LSCETVREQ.TNSIRKQW.ILKSH.EKL...VSKVHLE..
Retrocopy PREREDGSTGTVISDVEEDAGEMSRDSIWELSCETVREQPTNSIRKQWGILKSHGEKLGSYVSKVHLEN<

Parental  FNDEDVISRQDHEQETEKLELEIQQCKEMIKTQQQLLQQQLATACDDDTTSLLRDCYLLEEKERLKEEWS
          FNDED.IS.QDHEQE.EKL.LEIQ.CKEMIKTQQQLLQQ.L.T.CDDDTT.LL.DCYL..E.......W.
Retrocopy FNDEDLISKQDHEQEAEKLKLEIQKCKEMIKTQQQLLQQHLTTGCDDDTTALL*DCYL--EEKGCHKRWP

Parental  LFKEQKKNFERERRSFTEAAIRLGLERKAF
          LFKEQK.NF.RER.SF.EAAI.LGLERK.F
Retrocopy LFKEQKNNFQRER*SFIEAAIHLGLERKVF

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	62.86 RPM
SRP007412_cerebellum	0.00 RPM	49.90 RPM
SRP007412_heart	0.00 RPM	5.65 RPM
SRP007412_kidney	0.00 RPM	35.57 RPM
SRP007412_liver	0.00 RPM	9.46 RPM
SRP007412_testis	0.00 RPM	427.86 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1913 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1913 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1913 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2822
Pongo abelii	retro_pabe_2206

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000117155	1 retrocopy	retro_hsap_2822,
Pongo abelii	ENSPPYG00000001201	1 retrocopy	retro_pabe_2206,
Pan troglodytes	ENSPTRG00000000906	1 retrocopy	retro_ptro_1913 ,
Tarsius syrichta	ENSTSYG00000004276	1 retrocopy	retro_tsyr_526,
Tursiops truncatus	ENSTTRG00000008402	1 retrocopy	retro_ttru_1078,