RetrogeneDB ID: retro_pabe_1777

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:5009530..5010759(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSPPYG00000014852
• Aliases: None
• Description: SDA1 domain containing 1 [Source:HGNC Symbol;Acc:25537]

Sequence

>retro_pabe_1777
CCAGAGATGTTTAACTTTTCAGCCATTCACTTAATTCACGATCCCTAAGATTTTGCAGAAAAACTACTAAAGCAGCTTGA
GTGAAGTAAGGAGAGGTTTGAAGTAAAGATGATGCTCAGGAACCTCATCTCCAGATTGGTGGGAATTCATGAGCTCTTCC
TCTTCAATTTCTATCCTTTTTTGCAAAGGTTTCTGCAGCCCCACCAAAGAGAAGTAACAAAGATCCTCTGTTTGCTGCAC
AAGCATCTCATCACCTAGTACCCCCAGGGATTATTCAATCATTGCTTATGACTGTGGCAAAAAATTTTGTTACCGACAAG
AACTCTGGAGAAGTCATGACAGTAGAAATCAATGCTATAAAAGAGATAACAGCTCAATGTTCTCTGGCCATGACTGAAGA
ACTTCTCCAAGACCCGGCTCAGAATAAAACACACAAGGATAAAAATGTAATGATGTCTGCTAGAACTTTGATTCAGCTCT
TCCGAACACTGAATCCTCAGATGCTGCAGAAGAAATTCCGGGGTAACCCTACAGAGGCCTCCATAGAAGCAAGAGTACAA
GAATATGGAGAATTAGATGCTAAAGATTACATTCCAGGAGCAGAAGTTCTGGAAGGTGAGAAAGAAGAGAATGCTGAAAA
TGATGAAGATGGATGGGAAAATACCAGTCTCAGTGAGGAGGAGGAGGATGCTGATGGTGAATGGATTGATGTGCAACACT
CTTCCGATGAAGAACAGCAAGAAATCTCCAAGAAGCTGAACAGGATGCCCATGGAGGAGCGGAAAGCCAAAGCTGCAGCC
ATCAGCACCAGCCAAGTTTTAACTTAGGAAGACTTCCAGAAAATCCACATGGCCCAACTGAGAAAAGAACTTGATGCTGC
CCCTGGGAAATCCCAGAAGAGGAAATACACTGAAATAGACAGTGATGAAGAGCCCAGGGGTGAATTACTTTCTCTTCGGG
ACATTGAACGCCTTCATTAAAAGCCAAAGTCTGACAAAGAGACAAGACTAGCAACTGCAATGGCTAGAAAGACAGACTGA
TAAGAATTTGTGAGGAAGAAAACCAAAATGAATCTATTTTCTCGTTCGGCAAATAAAGAGAAGAAAAAACAGAAGAACTT
TATGATGATGCAGTATAGCCAGAATGTCCGGAGAAAAAATAAGTGTTCCTTCCAAGAAAAAGAGTTGGTGCTATGAGATG
CAGTTTTGAAAAAGAGAAAAAGAATGAAG

Alignment

ORF - retro_pabe_1777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.78 %
• Parental protein coverage: 59.53 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PEVFNFSAIHLIHDPQDFAEKLLKQLECCKERFEVKMMLMNLISRLVGIHELFLFNFYPFLQRFLQPHQR
          PE.FNFSAIHLIHDP.DFAEKLLKQLE..KERFEVKMML.NLISRLVGIHELFLFNFYPFLQRFLQPHQR
Retrocopy PEMFNFSAIHLIHDP*DFAEKLLKQLE*SKERFEVKMMLRNLISRLVGIHELFLFNFYPFLQRFLQPHQR

Parental  EVTKIL-LFAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLAMTEELLQDL
          EVTKIL.LFAAQASHHLVPP.IIQSLLMTVA.NFVTDKNSGEVMTV.INAIKEITA.C.LAMTEELLQD.
Retrocopy EVTKIL<LFAAQASHHLVPPGIIQSLLMTVAKNFVTDKNSGEVMTVEINAIKEITAQCSLAMTEELLQDP

Parental  AQYKTHKDKNVMMSARTLIHLFRTLNPQMLQKKFRGKPTEASIEARVQEYGELDAKDYIPGAEVLEVEKE
          AQ.KTHKDKNVMMSARTLI.LFRTLNPQMLQKKFRG.PTEASIEARVQEYGELDAKDYIPGAEVLE.EKE
Retrocopy AQNKTHKDKNVMMSARTLIQLFRTLNPQMLQKKFRGNPTEASIEARVQEYGELDAKDYIPGAEVLEGEKE

Parental  ENAENDEDGWESTSLSEEE-DADGEWIDVQHSSDEERQEISKKLNSMPMEERKAKAAAISTSRVLTQEDF
          ENAENDEDGWE.TSLSEEE.DADGEWIDVQHSSDEE.QEISKKLN.MPMEERKAKAAAISTS.VLT.EDF
Retrocopy ENAENDEDGWENTSLSEEEEDADGEWIDVQHSSDEEQQEISKKLNRMPMEERKAKAAAISTSQVLT*EDF

Parental  QKIRMAQMRKELDAAPGKSQKRKYIEIDSDEEPRGELLSLRDIERLHKKPKSDKETRLATAMAGKTDRKE
          QKI.MAQ.RKELDAAPGKSQKRKY.EIDSDEEPRGELLSLRDIERLH.KPKSDKETRLATAMA.KTD..E
Retrocopy QKIHMAQLRKELDAAPGKSQKRKYTEIDSDEEPRGELLSLRDIERLH*KPKSDKETRLATAMARKTD**E

Parental  FMRKKTKTNPFSSSTNKEKKKQKNFMMMRYSQNVRSKNKRSFREKQLALRDALLKKRKRMK
          F.RKKTK.N.FS.S.NKEKKKQKNFMMM.YSQNVR.KNK.SF.EK.L.L.DA.LKKRKRMK
Retrocopy FVRKKTKMNLFSRSANKEKKKQKNFMMMQYSQNVRRKNKCSFQEKELVL*DAVLKKRKRMK

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	16.03 RPM
SRP007412_cerebellum	0.00 RPM	19.82 RPM
SRP007412_heart	0.00 RPM	9.03 RPM
SRP007412_kidney	0.00 RPM	16.47 RPM
SRP007412_liver	0.00 RPM	17.29 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1777 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1777 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1777 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2412
Pan troglodytes	retro_ptro_1388
Gorilla gorilla	retro_ggor_1498
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,