RetrogeneDB ID: retro_ptro_2732

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:22673000..22674221(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSPTRG00000024399
• Aliases: None
• Description: SDA1 domain containing 1 [Source:HGNC Symbol;Acc:25537]

Sequence

>retro_ptro_2732
GAGGTGTTTAACTTTTTAGCCGTTCACTTGATTCATGATCCCCAAAATTTTGCAGAAAAACTATTAAAGCAGCTTGAGTG
CTGTAAGGAGAGGTTGGAAGTGAAGATGATGCTCATGAACCTCATCTCAGATTGGTGGGAATTCATAAGCTCTTCCTCTT
CAATTTCTATCACTTTTTGCGAAGGTTTCTGCAGCCCCACCAAAGAGAAGTAACAAAGAACCTTCTGTTTGCTGCACAAG
CATCTCATCACCTAGTACACCCAGCGATTATTCAATCATTGCTTATGACTGTGGCCAACAATTTTGTTAACGACAAGAAC
TCTGGAGAAGCCATGACAATAGGAATCAATGCTGTAAAAGAGACAACAGCTCAGTGTCCTCTGGCCATGACTGAAAAGCT
TCTCCAAGACCTGGCTCAGTATAAAACACACAAGGATAATAATGTAATGATGTCTGCTAGAACTTTGATTCGGCTCTTCC
GAACACTGAATCCTCAGATGCTGCAGAAGAAATTCTGGGGTAAGCCTACAGAAGCCTCCATAGAAGCAAGAGTACAAAAT
ATGGAGAATTAGATGCTAAAGATTACATTCCAGGAGCAGAAGTTCTGGAAGTTGAGAAAGAGGAGAGTGCTGAAAATGAT
GAAGATGGATGGGAAAGTACCAGTCTCAGTGAGGAGGAGGATGCCGATGGCGAATGGGTTGATGTGCAACACTCTTCCAA
TGAAGAACAGCAAGAAATTTCCAAGAAGCTGAACAGCATGCCCATGGAGGAGCAGAAAGCCAAAACTGCAGCCGTCAGCA
CCAGTCGAGTTTTAAGTTAGGAAGACTTCCAGAAAATCCACATGGCGCAAATGAGAAAAGAACTTGACGCTGTCCCCCGG
GAAATCCCAGAAGAGGAAATATATTGAAATCGACAGTGATGAAGAGCCGAGGGGTGAATTACTTTCTCTTCCAGACATTG
AACGCCTTCATAAAAAGCCAAAGTCTGACAAAGAGACAAGACTAGCAACTGCAATGGCTGGAAAGACAGACCGAAAAGAA
TTTGTGAGGAAGAAAACCAAAGTGAATCCATTTTCCAGTTCAAAAAGTAAAGAGAAGAAAAAACAGAAGAACTTTATGAT
GATGTGGTATAGCCAGAACGTCTGGTCAAAAAATAAGCGTTCCTTCTGAGAAAAACAATTGGCGCTGCGAGATGCCTTTT
GAAAAGAGAAAAAGAATGAAG

Alignment

ORF - retro_ptro_2732 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.59 %
• Parental protein coverage: 59.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EVFNFSAIHLIHDPQDFAEKLLKQLECCKERFEVKMMLMNLIS-RLVGIHELFLFNFYPFLQRFLQPHQR
          EVFNF.A.HLIHDPQ.FAEKLLKQLECCKER.EVKMMLMNLIS.RLVGIH.LFLFNFY.FL.RFLQPHQR
Retrocopy EVFNFLAVHLIHDPQNFAEKLLKQLECCKERLEVKMMLMNLIS<RLVGIHKLFLFNFYHFLRRFLQPHQR

Parental  EVTKILLFAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLAMTEELLQDLA
          EVTK.LLFAAQASHHLV.P.IIQSLLMTVANNFV.DKNSGE.MT.GINA.KE.TA.CPLAMTE.LLQDLA
Retrocopy EVTKNLLFAAQASHHLVHPAIIQSLLMTVANNFVNDKNSGEAMTIGINAVKETTAQCPLAMTEKLLQDLA

Parental  QYKTHKDKNVMMSARTLIHLFRTLNPQMLQKKFRGKPTEASIEARVQ-EYGELDAKDYIPGAEVLEVEKE
          QYKTHKD.NVMMSARTLI.LFRTLNPQMLQKKF.GKPTEASIEARVQ..YGELDAKDYIPGAEVLEVEKE
Retrocopy QYKTHKDNNVMMSARTLIRLFRTLNPQMLQKKFWGKPTEASIEARVQ<KYGELDAKDYIPGAEVLEVEKE

Parental  ENAENDEDGWESTSLSEEEDADGEWIDVQHSSDEEQQEISKKLNSMPMEERKAKAAAISTSRVLTQEDFQ
          E.AENDEDGWESTSLSEEEDADGEW.DVQHSS.EEQQEISKKLNSMPMEE.KAK.AA.STSRVL..EDFQ
Retrocopy ESAENDEDGWESTSLSEEEDADGEWVDVQHSSNEEQQEISKKLNSMPMEEQKAKTAAVSTSRVLS*EDFQ

Parental  KIRMAQMRKELDA-APGKSQKRKYIEIDSDEEPRGELLSLRDIERLHKKPKSDKETRLATAMAGKTDRKE
          KI.MAQMRKELDA..PGKSQKRKYIEIDSDEEPRGELLSL.DIERLHKKPKSDKETRLATAMAGKTDRKE
Retrocopy KIHMAQMRKELDA>SPGKSQKRKYIEIDSDEEPRGELLSLPDIERLHKKPKSDKETRLATAMAGKTDRKE

Parental  FVRKKTKTNPFSSSTNKEKKKQKNFMMMRYSQNVRSKNKRSFREKQLALRDA-LLK-KRKRMK
          FVRKKTK.NPFSSS..KEKKKQKNFMMM.YSQNV.SKNKRSF.EKQLALRDA.LLK.KRKRMK
Retrocopy FVRKKTKVNPFSSSKSKEKKKQKNFMMMWYSQNVWSKNKRSF*EKQLALRDA<LLK<KRKRMK

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	0.86 RPM	26.78 RPM
SRP007412_cerebellum	0.57 RPM	36.60 RPM
SRP007412_heart	1.34 RPM	18.92 RPM
SRP007412_kidney	1.33 RPM	28.45 RPM
SRP007412_liver	0.33 RPM	25.21 RPM
SRP007412_testis	5.16 RPM	84.52 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2732 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2732 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2732 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4030

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008524	2 retrocopies	retro_cpor_510, retro_cpor_994,
Homo sapiens	ENSG00000198301	2 retrocopies	retro_hsap_2412, retro_hsap_4030,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Oryctolagus cuniculus	ENSOCUG00000026953	1 retrocopy	retro_ocun_547,
Pongo abelii	ENSPPYG00000014852	1 retrocopy	retro_pabe_1777,
Pan troglodytes	ENSPTRG00000024399	2 retrocopies	retro_ptro_1388, retro_ptro_2732 ,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Tupaia belangeri	ENSTBEG00000005270	1 retrocopy	retro_tbel_2414,