RetrogeneDB ID: retro_pabe_3785

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:84067773..84068818(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS31
• Ensembl ID: ENSPPYG00000005306
• Aliases: None
• Description: mitochondrial ribosomal protein S31 [Source:HGNC Symbol;Acc:16632]

Sequence

>retro_pabe_3785
ATGTTTCCTAGACTCTCGACATTCCTATCTCCTCGCCTCCTTTCCCGCCACTCTTTGTCCTCTGGAAGCCCGGAGACATC
AGCTGCTGCGATTGTACTACTGGCTGTTCAGCACGGAGCGGTTAGGACAAAAAATAAATTCAAAGATATTTTGGCACTAA
CAGCATGATCTGTAGCAAGAAAGATGAGCAGTCTGTTCAAACCGATGAGACTTCCAAGGAGACTTCAGAGAGCCAAGGCA
GTGAAAAGGAAAATACGAGAAAGACTTGTTAAACATTATTAAGGGCATGAAAGTTGAATTAAGCACAGTAAACGTACCAA
CAACAAAGCCCCTCAACAGAAGACCACTTAAAACTTTGGAAGCTACACTTGGCAGTCTTCAAAGAGCTACAGAACATGCT
CCAAAGAAGAGAATTGGAGCCCGAGTCTTGAGTTGGTGGCAGCTGAATCTGGTGCGGCAGATTCTCTCCCTTTTGACAAG
CAAACAACCAAGTCAGAGCTGCTGAGGCAGCTCCAGCAGCATTAGGAAGAGTCAAGGGCATAGAGAGATGCAGAGAGACC
TAAAATTAGTTTCAGTAACATAATATAGATAAGAAAGTTGCCAGACTTGCTACAGCTAGAGTTTGTTCAAGACCAGAGCA
TCAGATTCAGTTTGACAAAGGCTATGACAATTATCCTGGCCAGGAGAAGACCTATGATCTTAGAAAAAGATGTAGGAAAA
ATATATTCACGGGGAAAAGACTTAATATTTTTGACATGACGGCAGTTACTAAACAAGCACCTGAAACAGACATATCACCT
TCACTTTTGGATGTGGAATTTGCTAAGCAGTTAGTGAACAACCCCTTCAGAATGGGTTTGAAAAGTTGATCCAGTGGACA
AAAGAGGGGAAATTGTGGGAGTTCCCAATTAACAATGAAGCAGGTTTTGATGATGGTTCAGAATTTCGTGAACATATATT
TCTGGAGAAACATCTGAAGGGCTTTCCAAAACAAGGACCAATTCACCACTTCATGGAGCTGATGACTTGTGGCCTTTCCA
AAAAC

Alignment

ORF - retro_pabe_3785 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.94 %
• Parental protein coverage: 91.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MFPRVSTFLPLRLLSRHPLSSGSPETSAAAIMLLAVRHGTVRTKNN-IQRYFGTNSVICSKKDKQSVRTD
          MFPR.STFL..RLLSRH.LSSGSPETSAAAI.LLAV.HG.VRTKN..IQRYFGTNS.ICSKKD.QSV.TD
Retrocopy MFPRLSTFLSPRLLSRHSLSSGSPETSAAAIVLLAVQHGAVRTKNK<IQRYFGTNSMICSKKDEQSVQTD

Parental  ETSKETSESQDGEKENTKK-DLLGIIKGMKVELSTVNVQTTKPPKRRPLKSLETTVGRLRRATEYAPKKR
          ETSKETSESQ..EKENT.K.DLL.IIKGMKVELSTVNV.TTKP..RRPLK.LE.T.G.L.RATE.APKKR
Retrocopy ETSKETSESQGSEKENTRK<DLLNIIKGMKVELSTVNVPTTKPLNRRPLKTLEATLGSLQRATEHAPKKR

Parental  IEPL-SPELVAAASAVADSLPFDKQTTKSELLSQLQQHEEESRAQRDAERPKISFSNII-SDMKVARSAT
          I....S.ELVAA.S..ADSLPFDKQTTKSELL.QLQQH.EESRA.RDAERPKISFSNII..D.KVAR.AT
Retrocopy IGAR<SLELVAAESGAADSLPFDKQTTKSELLRQLQQH*EESRA*RDAERPKISFSNII<IDKKVARLAT

Parental  ARVRSRPELQIQFDEGYDNYPGQEETDDHKK--RKNIFRGKRLNIFDMMAVTKEAPETDTSPSLWDVEFA
          ARV.SRPE.QIQFD.GYDNYPGQE.T.D..K..RKNIF.GKRLNIFDM.AVTK.APETD.SPSL.DVEFA
Retrocopy ARVCSRPEHQIQFDKGYDNYPGQEKTYDLRKRCRKNIFTGKRLNIFDMTAVTKQAPETDISPSLLDVEFA

Parental  KQLATVNEQPLQNG-FEELIQWTKEGKLWEFPINNEAGFDDDGSEFHEHIFLEKHLESFPKQGPIRHFME
          KQL......P...G.FE.LIQWTKEGKLWEFPINNEAGF.DDGSEF.EHIFLEKHL..FPKQGPI.HFME
Retrocopy KQLV---NNPFRMG<FEKLIQWTKEGKLWEFPINNEAGF-DDGSEFREHIFLEKHLKGFPKQGPIHHFME

Parental  LVTCGLSKN
          L.TCGLSKN
Retrocopy LMTCGLSKN

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	7.80 RPM
SRP007412_cerebellum	0.00 RPM	12.16 RPM
SRP007412_heart	0.00 RPM	6.11 RPM
SRP007412_kidney	0.00 RPM	9.48 RPM
SRP007412_liver	0.00 RPM	10.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3785 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3785 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3785 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008470	1 retrocopy	retro_chof_586,
Equus caballus	ENSECAG00000003600	1 retrocopy	retro_ecab_1028,
Nomascus leucogenys	ENSNLEG00000001164	1 retrocopy	retro_nleu_1999,
Oryctolagus cuniculus	ENSOCUG00000021467	1 retrocopy	retro_ocun_1747,
Otolemur garnettii	ENSOGAG00000024374	1 retrocopy	retro_ogar_914,
Ochotona princeps	ENSOPRG00000014606	1 retrocopy	retro_opri_1137,
Pongo abelii	ENSPPYG00000005306	1 retrocopy	retro_pabe_3785 ,
Sorex araneus	ENSSARG00000004428	1 retrocopy	retro_sara_594,
Sarcophilus harrisii	ENSSHAG00000007140	1 retrocopy	retro_shar_591,
Tarsius syrichta	ENSTSYG00000002170	1 retrocopy	retro_tsyr_238,
Tursiops truncatus	ENSTTRG00000012556	1 retrocopy	retro_ttru_1285,