RetrogeneDB ID: retro_pabe_244

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:62828551..62829156(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIF3L1
• Ensembl ID: ENSPPYG00000013063
• Aliases: None
• Description: NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:13390]

Sequence

>retro_pabe_244
ACCGAAGACCTGGACAAAGTCATGTCTGCAGTGAAGAAAAGTTGTGAATATTTCTGTCACTTCTTTGTCTGCTGGGATTG
ATAATGAAAAACAAACATGACTCAGTCTCAATTATACTTAGAAGACTTTGATGCAGGTAGTGGCTTTTCTCTCCCAGAAC
ATAAAATGACATCAGAAGACTGAAATTATGTACTGGAGAAGCCTTTGCTTCTACATACTGGAATGGGACGGTTATGCATA
GTGGATGAATCTATCTCCCTGACAGCTATGACTGAGCCAATCACAAACTGCTTAAAACTATCACATATGTGCTTAGTTCT
TAGAGTAGGGAGGACCGAAGGTTCTAAAGTCAAAGTCGTGGCCCTGTGTGCTGATTCTGGGAGCAGTGTTCTGCAGAGTA
TAGAAGCTGACCTTTACCTCCCAGGTGGGATGTCTCATCATAATATTCTGAATGCTGCTTCCTAAGGAATAAATGTCATC
CTTTATGAACTCAGCAACACTGAATAAGACTTTCTTTCTGACATTTGAGATATACTGTGTGCTTACTTGAAGAGTAAGAT
TAATATTATCCTTCAGAGACAAGCAAGGACCCTCTTTATGTAGTA

Alignment

ORF - retro_pabe_244 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.37 %
• Parental protein coverage: 53.58 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TQDLDKVMSAVKG-IDGVSVTSFSARTGNEEQTRINLNCTQKALMQVVDFLSRNKQLYQKTEILS-LEKP
          T.DLDKVMSAVK......SVTS.SA...NE.QT...LN.T.K.LMQVV.FLS.N....QKTEI...LEKP
Retrocopy TEDLDKVMSAVKK>VVNISVTSLSAGIDNEKQT*LSLNYT*KTLMQVVAFLSQNIK*HQKTEIMY<LEKP

Parental  LLLHTGMGRLCTLDESVCLATMIDRIKRHLKLSHIRLALGVGRTLESQVKVVALCAGSGSSVLQGVEADL
          LLLHTGMGRLC..DES..L..M...I...LKLSH..L.L.VGRT..S.VKVVALCA.SGSSVLQ..EADL
Retrocopy LLLHTGMGRLCIVDESISLTAMTEPITNCLKLSHMCLVLRVGRTEGSKVKVVALCADSGSSVLQSIEADL

Parental  YLTGEMSHHDILDAASQGINVIVCEHSNTERGFLSDLRDMLGSHLENKINIIL-SETDRDPLQVV
          YL.G.MSHH.IL.AAS.GINVI..E.SNTE..FLSD..D.L...L..KINIIL.SET..DPL.VV
Retrocopy YLPGGMSHHNILNAAS*GINVILYELSNTE*DFLSDI*DILCAYLKSKINIIL<SETSKDPLYVV

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	12.55 RPM
SRP007412_cerebellum	0.00 RPM	15.81 RPM
SRP007412_heart	0.00 RPM	4.03 RPM
SRP007412_kidney	0.00 RPM	9.88 RPM
SRP007412_liver	0.00 RPM	5.78 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_244 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_244 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_244 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_444

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023186	1 retrocopy	retro_fcat_589,
Macaca mulatta	ENSMMUG00000006639	1 retrocopy	retro_mmul_444,
Nomascus leucogenys	ENSNLEG00000006935	1 retrocopy	retro_nleu_1504,
Oryctolagus cuniculus	ENSOCUG00000010667	16 retrocopies	retro_ocun_1105, retro_ocun_1534, retro_ocun_1539, retro_ocun_1691, retro_ocun_1692, retro_ocun_1710, retro_ocun_1729, retro_ocun_1749, retro_ocun_1789, retro_ocun_1828, retro_ocun_1837, retro_ocun_1841, retro_ocun_1846, retro_ocun_1847, retro_ocun_1854, retro_ocun_929,
Pongo abelii	ENSPPYG00000013063	1 retrocopy	retro_pabe_244 ,
Tupaia belangeri	ENSTBEG00000000704	1 retrocopy	retro_tbel_3512,