RetrogeneDB ID: retro_pabe_2206

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:29512335..29513252(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSX2IP
• Ensembl ID: ENSPPYG00000001201
• Aliases: None
• Description: synovial sarcoma, X breakpoint 2 interacting protein [Source:HGNC Symbol;Acc:16509]

Sequence

>retro_pabe_2206
AGACAGTTACAATGCAAGAACAGGAATTTGAATCAGCTATTGAAAAATGAGAAGGATGAGGTACAGAAATTACAAAATAT
TATTGTAAGTTGAGCTATTCAGTATTATCATGATATGATATAAAAAGAGTGTGAACATAACAAACTGAAGGAAAGTCTAC
ATCAACTTTCTATGAGCAAAAAAGAATTAAAAATAGCTTTAGACATTTTAAATAATGTGGGGAGAGCTGACGGAAAAAGA
GGCCTCTGGAAAACTGGTAAGACAGAAGTCAGGAATGAGATGAAATTTATAAAATTATCTTGAATGATTATGAGTATTGT
CACAAACAATTCCTAATGGAAAATGCTGATAATGAAGAAGTTTCTTCACCAAATGGAAAAGGATATGTTTTTTCTTCTTT
CTCCTCAAAAGAAACCTAGAGAAAGAGAAGATGGTAGTACAGGAACTGTCATCTCAGATGTTGAAGAAGATGCTGGGGAA
ATGAGCAGAGACAGTATCTGGGACCTTTCCTGTGAAACTGTGAGAGAACGGCCTACAAGCAGCATCAGAAAACAGTAGGG
AATTTTGAAAAGTCACGGAGAAAAACTTGGTAGCCACTTTTCAAAGATACACTTAGAAAATTTAATGATGAAGATTTAAT
CTCAAAACAAGACCATGCACAGGAAGCTGAAAAACTCAAATTAGAAATTCAGAAATGTAAAGAAATGATTAAAACTCAGC
AGCAACTTTTACAACAACCCCTCACTACTGCTTGTGATGATGATACCACTGCACTATTATGAGACTGTTATTTGGAAGGA
AAGGGATGCCACAAACAATGGTCCCTTTTTAAAGAGCAAAAAAAAAATAATTTTCAGAGAGAAAGATGAAGCTTTACAGA
AGCCACTATTCACCTAGGTTTGGAGAGAAAGGTGTTT

Alignment

ORF - retro_pabe_2206 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.04 %
• Parental protein coverage: 50.16 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RQLQCKNRNLHQLLKNEKDEVQKLQNIIASRATQYNHDMKRKEREYNKLKERLHQLVMNKKDKKIAMDIL
          RQLQCKNRNL.QLLKNEKDEVQKLQNII.S.A.QY.HDM..KE.E.NKLKE.LHQL.M.KK..KIA.DIL
Retrocopy RQLQCKNRNLNQLLKNEKDEVQKLQNIIVS*AIQYYHDMI*KECEHNKLKESLHQLSMSKKELKIALDIL

Parental  NYVGRADGKRGSWRTGKTEARNE-DEMYKILLNDYEYRQKQILMENAE-LKKVLQQMKKEMISLLSPQKK
          N.VGRADGKRG.W.TGKTE.RNE.DE.YKI.LNDYEY..KQ.LMENA...KK.L.QM.K.M..LLSPQ.K
Retrocopy NNVGRADGKRGLWKTGKTEVRNE<DEIYKIILNDYEYCHKQFLMENAD>MKKFLHQMEKDMFFLLSPQ-K

Parental  KPRERVDDSTGTVISDVEEDAGELSRESMWDLSCETVREQLTNSIRKQWRILKSHVEKLDNQVSKVHLEG
          KPRER.D.STGTVISDVEEDAGE.SR.S.WDLSCETVRE..T.SIRKQ..ILKSH.EKL....SK.HLE.
Retrocopy KPREREDGSTGTVISDVEEDAGEMSRDSIWDLSCETVRERPTSSIRKQ*GILKSHGEKLGSHFSKIHLEN

Parental  -FNDEDVISRQDHEQETEKLELEIQQCKEMIKTQQQLLQQQLATACDDDTTSLLRDCYLLEEKERLKEEW
          .FNDED.IS.QDH.QE.EKL.LEIQ.CKEMIKTQQQLLQQ.L.TACDDDTT.LL.DCYL..E.......W
Retrocopy <FNDEDLISKQDHAQEAEKLKLEIQKCKEMIKTQQQLLQQPLTTACDDDTTALL*DCYL--EGKGCHKQW

Parental  SLFKE-QKKNFERERRSFTEAAIRLGLERKAF
          SLFKE....NF.RER.SFTEA.I.LGLERK.F
Retrocopy SLFKEXXXXNFQRER*SFTEATIHLGLERKVF

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	46.94 RPM
SRP007412_cerebellum	0.00 RPM	63.84 RPM
SRP007412_heart	0.00 RPM	4.67 RPM
SRP007412_kidney	0.00 RPM	11.97 RPM
SRP007412_liver	0.00 RPM	6.92 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2206 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2206 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2206 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2822
Pan troglodytes	retro_ptro_1913

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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,