RetrogeneDB ID: retro_pabe_193

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:96454169..96454691(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020534
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NDUFS4
• Ensembl ID: ENSPPYG00000015455
• Aliases: None
• Description: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P0CB95]

Sequence

>retro_pabe_193
GCAGGATTCTCAACGTCAGTGGCACTGAGGCAGACGTTGTGGCGGAGAAGGGCAGTGGCTGTAGCTGCCCTTTCCGTTTC
CAGGGTTCTGACCAGGTCCTTGAGGACTTCCACATGGAGATTGGCACAGGACCAGACTCAAGACACACAACTCATAACAG
TTGATGAAAAATTGGCTATCACTACTTTAACTGGTGTTCCAGAAGAGCATATAAAAACTAGAAAAGTCAGGGTCTTTGTT
CCTGCTCGCAATAACATGCAGTCTGGAGTAAACAACACAAAGAAATGGAAGATGGAGTTTGATACCAGGGAGCGATGGGA
AAATCCTTTGATGGGTTGGGCATCAACGGCTGATCCCTTATCCAACATGGTTCCAAGCTTCCGTACTAAAGAAGATGCAG
TTTCCTTTGCAGAAAAAAATGGATGGAGCTATGACGTTGAAGAGAGGAAGTTTCCAAAACCCAAGTCCAGGTCTTATGGT
GCAAACTTTTCTTGGAAGAAAAGAACAAGAGTATCCACAAAA

Alignment

ORF - retro_pabe_193 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.1 %
• Parental protein coverage: 99.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAVSMSVALRQTLWRRRAVAVAALSVSRVPTRLLRTSTWRLAQDQTQDTQLITVDEKLDITTLTGVPEEH
          A..S.SVALRQTLWRRRAVAVAALSVSRV.TR.LRTSTWRLAQDQTQDTQLITVDEKL.ITTLTGVPEEH
Retrocopy AGFSTSVALRQTLWRRRAVAVAALSVSRVLTRSLRTSTWRLAQDQTQDTQLITVDEKLAITTLTGVPEEH

Parental  IKTRKVRIFVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWASTADPLSNMVLTFRTKEDAVSFAEKN
          IKTRKVR.FVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWASTADPLSNMV..FRTKEDAVSFAEKN
Retrocopy IKTRKVRVFVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWASTADPLSNMVPSFRTKEDAVSFAEKN

Parental  GWSYDVEERKVPKPKSKSYGANFSWNKRTRVSTK
          GWSYDVEERK.PKPKS.SYGANFSW.KRTRVSTK
Retrocopy GWSYDVEERKFPKPKSRSYGANFSWKKRTRVSTK

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	13.38 RPM
SRP007412_cerebellum	0.00 RPM	28.70 RPM
SRP007412_heart	0.06 RPM	46.72 RPM
SRP007412_kidney	0.00 RPM	25.36 RPM
SRP007412_liver	0.00 RPM	20.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_193 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_193 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005452	1 retrocopy	retro_cpor_1111,
Erinaceus europaeus	ENSEEUG00000015851	3 retrocopies	retro_eeur_133, retro_eeur_30, retro_eeur_347,
Macropus eugenii	ENSMEUG00000001362	1 retrocopy	retro_meug_651,
Microcebus murinus	ENSMICG00000015138	1 retrocopy	retro_mmur_355,
Monodelphis domestica	ENSMODG00000019465	1 retrocopy	retro_mdom_1227,
Mus musculus	ENSMUSG00000021764	1 retrocopy	retro_mmus_3372,
Ochotona princeps	ENSOPRG00000013784	1 retrocopy	retro_opri_508,
Procavia capensis	ENSPCAG00000013496	1 retrocopy	retro_pcap_268,
Pongo abelii	ENSPPYG00000015455	1 retrocopy	retro_pabe_193 ,
Sus scrofa	ENSSSCG00000016893	1 retrocopy	retro_sscr_999,
Tupaia belangeri	ENSTBEG00000004605	1 retrocopy	retro_tbel_2068,