RetrogeneDB ID: retro_pabe_1780

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:8947693..8948155(+)
• Located in intron of: ENSPPYG00000010718

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIMP1
• Ensembl ID: ENSPPYG00000014981
• Aliases: AIMP1, SCYE1
• Description: aminoacyl tRNA synthase complex-interacting multifunctional protein 1 [Source:RefSeq peptide;Acc:NP_001126507]

Sequence

>retro_pabe_1780
AAAAAACAGCAATCAGTAGCAGGAAGCACCAACTGTAAGCCAATAAATGTTTCCCATCTAGATATTTGAATTGGTTGCAT
CATAACTGTCAGAAAACACCCTGATGCAGATTCTTTGTATGTAGAAGATGTAGTTGTTGGGGAAATAGTCCCAAGAACAG
TTGTCAGTGGTCTGGAGAATGATGTTCCTCTTGAACAGGTGCAAAATCAGATGGTGATTTTACTTTGTAACCTGAAACCT
ACAAAGATGAGGGGAGTATTATCTCATGCAGTGATCATGTGTGCTTGTTCACCAGAGAAAGTTGAAATCTTGGCCCTTCC
TAATGGAGACAGAATTACTTTTGATGCTTTCCCTGGAGAGCCCAACAAGGAACCAAGTCCTAAGAAGACTGGGGAGCAGA
TCCCACCTCATTTTTATACTATGATGAGTGTGTGGCTGTATACAAAGGAGCTCCCTTTGAGA

Alignment

ORF - retro_pabe_1780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.96 %
• Parental protein coverage: 52.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKQQSIAGSADSKPIDVSRLDLRIGCIITARKHPDADSLYVEEVDVGEIAPRTVVSGLVNHVPLEQMQNR
          KKQQS.AGS...KPI.VS.LD..IGCIIT.RKHPDADSLYVE.V.VGEI.PRTVVSGL.N.VPLEQ.QN.
Retrocopy KKQQSVAGSTNCKPINVSHLDI*IGCIITVRKHPDADSLYVEDVVVGEIVPRTVVSGLENDVPLEQVQNQ

Parental  MVILLCNLKPAKMRGVLSQAMVMCASSPEKIEILAPPNGSVPGDRITFDAFPGEPDKELNPKKRFGSRSS
          MVILLCNLKP.KMRGVLS.A..MCA.SPEK.EILA.PNG....DRITFDAFPGEP.KE..PKK..G....
Retrocopy MVILLCNLKPTKMRGVLSHAVIMCACSPEKVEILALPNG----DRITFDAFPGEPNKEPSPKKT-GEQIP

Parental  LIFTLTMSVWLHTKEFPLR
          ..F...MSVWL.TKE.PLR
Retrocopy PHFYTMMSVWLYTKELPLR

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	0.06 RPM	20.62 RPM
SRP007412_cerebellum	0.24 RPM	22.74 RPM
SRP007412_heart	0.12 RPM	23.27 RPM
SRP007412_kidney	0.10 RPM	20.58 RPM
SRP007412_liver	0.00 RPM	18.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1780 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1780 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_2504

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000619	2 retrocopies	retro_chof_1176, retro_chof_2050,
Callithrix jacchus	ENSCJAG00000015885	1 retrocopy	retro_cjac_2504,
Dipodomys ordii	ENSDORG00000005018	1 retrocopy	retro_dord_540,
Mustela putorius furo	ENSMPUG00000008952	1 retrocopy	retro_mputfur_1606,
Mus musculus	ENSMUSG00000028029	2 retrocopies	retro_mmus_2271, retro_mmus_3334,
Pongo abelii	ENSPPYG00000014981	1 retrocopy	retro_pabe_1780 ,
Rattus norvegicus	ENSRNOG00000011384	1 retrocopy	retro_rnor_1704,
Ictidomys tridecemlineatus	ENSSTOG00000008178	1 retrocopy	retro_itri_1173,
Tupaia belangeri	ENSTBEG00000004412	1 retrocopy	retro_tbel_4008,