RetrogeneDB ID: retro_ptro_1388

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:10270507..10271662(+)
• 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_1388
CAGCTTGAGTGAAGTAAGGAGAAGTTTGACGTGAAAATGATGCTCATGAACCTCATCTCCAGATTGGTGGGAATTCATGA
GCTCTTTCTCTTCAATTTCTATCCTTGTTTGCAAAGGTTTCTGCAGCCCCACCAAAGAGAAGTAACAAAGATCCTCCGTT
TGCTGCACAAGCATCTCATCACCTAGTACCCCCAGAGATTATTCAATCATTGCTTACGACTCTGGCAAACAATTTGGTTA
CCGACAAGAACTCTGGAGAAGTCATGACAGTAGGAATCAATGCTATAAAAGAGATAACAGCTCGATGTTCTCTGGCCATG
ACTGAAGAACTTCTCCAAGACCTGGCTCAGTATAAAACACACAAGGATAAGAATGTAATGATGTGTGCTAGAACTTTGAT
TCAGCTCTTCCAAACACTGAATCCTCAGATGCTGCAGAAGAAATTCCAGGGTAAGCCTACAGAGGCCTCCATAGAAGCAA
GAGTACAAGAATATGGAGAATTAGATGCTAAAGATTACATTCCAGGAGCAGAAGTTCTGGAAGGTGAGAAAGAAAAGAAT
GCTGAAAATGATGAAGATGGATGGGAAAATACCAGTCTCAGTGAGGAGGAGGATGCTATTGGTGAATGGATTGATGTGCA
ACACTCTTCTGATGAAGAACAGCAAGAAATCTCCAAGAAGCTGAACAGGATGCCCATGGAGGAGCAGAAAGACAAAGCTG
CAGCCATCAGCACCAGCCAAGTTTTAACTCAGGAAGACTTCCAGAAAATCCGCATGGCCCAACTGAGAAAAGAACTTGAT
ACTGCCCCTGGAAAATCCCAGAAGAGGAAATAAATTGAAATAGACAGTGATGAAGAGCCCAGGGGTGAATTACTTTCTCT
TCGGGACATTGAACGCCTTCATTAAAAGCCGAAGTCTGACAAAGAGACAAGACTAGCAACTGCAATGGCTAGAAAGACAG
ACCGAAAAGAATTTGTGAGGAAGAAAACCAAAATGAATCCATTTCCCAGTTTGACAAATAAAGAGAAGAAAAAAACAGAA
GAACTTTATGATGATGCAGTATAGCCAGAATGTCCGGTGAAAAAATAAGCGTTCCTTCCGAGAAAAACAGTTGGCGCTAC
GAGATGCACTTTTGAAAAAGAGAAAAAGAATGAAG

Alignment

ORF - retro_ptro_1388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.21 %
• Parental protein coverage: 56.04 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QLECCKERFEVKMMLMNLISRLVGIHELFLFNFYPFLQRFLQPHQREVTKILL-FAAQASHHLVPPEIIQ
          QLE..KE.F.VKMMLMNLISRLVGIHELFLFNFYP.LQRFLQPHQREVTKIL..FAAQASHHLVPPEIIQ
Retrocopy QLE*SKEKFDVKMMLMNLISRLVGIHELFLFNFYPCLQRFLQPHQREVTKILR<FAAQASHHLVPPEIIQ

Parental  SLLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLAMTEELLQDLAQYKTHKDKNVMMSARTLIHLFRT
          SLL.T.ANN.VTDKNSGEVMTVGINAIKEITARC.LAMTEELLQDLAQYKTHKDKNVMM.ARTLI.LF.T
Retrocopy SLLTTLANNLVTDKNSGEVMTVGINAIKEITARCSLAMTEELLQDLAQYKTHKDKNVMMCARTLIQLFQT

Parental  LNPQMLQKKFRGKPTEASIEARVQEYGELDAKDYIPGAEVLEVEKEENAENDEDGWESTSLSEEEDADGE
          LNPQMLQKKF.GKPTEASIEARVQEYGELDAKDYIPGAEVLE.EKE.NAENDEDGWE.TSLSEEEDA.GE
Retrocopy LNPQMLQKKFQGKPTEASIEARVQEYGELDAKDYIPGAEVLEGEKEKNAENDEDGWENTSLSEEEDAIGE

Parental  WIDVQHSSDEEQQEISKKLNSMPMEERKAKAAAISTSRVLTQEDFQKIRMAQMRKELDAAPGKSQKRKYI
          WIDVQHSSDEEQQEISKKLN.MPMEE.K.KAAAISTS.VLTQEDFQKIRMAQ.RKELD.APGKSQKRK.I
Retrocopy WIDVQHSSDEEQQEISKKLNRMPMEEQKDKAAAISTSQVLTQEDFQKIRMAQLRKELDTAPGKSQKRK*I

Parental  EIDSDEEPRGELLSLRDIERLHKKPKSDKETRLATAMAGKTDRKEFVRKKTKTNPFSSSTNKEK-KKQKN
          EIDSDEEPRGELLSLRDIERLH.KPKSDKETRLATAMA.KTDRKEFVRKKTK.NPF.S.TNKEK.KKQKN
Retrocopy EIDSDEEPRGELLSLRDIERLH*KPKSDKETRLATAMARKTDRKEFVRKKTKMNPFPSLTNKEK>KKQKN

Parental  FMMMRYSQNVRSKNKRSFREKQLALRDALLKKRKRMK
          FMMM.YSQNVR.KNKRSFREKQLALRDALLKKRKRMK
Retrocopy FMMMQYSQNVR*KNKRSFREKQLALRDALLKKRKRMK

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	0.02 RPM	26.78 RPM
SRP007412_cerebellum	0.04 RPM	36.60 RPM
SRP007412_heart	0.00 RPM	18.92 RPM
SRP007412_kidney	0.03 RPM	28.45 RPM
SRP007412_liver	0.00 RPM	25.21 RPM
SRP007412_testis	0.42 RPM	84.52 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1388 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1388 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1388 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2412
Gorilla gorilla	retro_ggor_1498
Pongo abelii	retro_pabe_1777
Macaca mulatta	retro_mmul_604

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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,