RetrogeneDB ID: retro_pabe_2021

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a_random:3857854..3858432(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB4
• Ensembl ID: ENSPPYG00000013047
• Aliases: MOB4, MOB3, MOBKL3, PHOCN, PREI3
• Description: MOB-like protein phocein [Source:UniProtKB/Swiss-Prot;Acc:Q5RDB1]

Sequence

>retro_pabe_2021
ATGGACAGTACACTAGCTGCTCAACAGTCTATTCAACAGAACGTAAGAGCAGATTGCTCCAATATTGACAAAATCTGAAG
CACTTAAAGGCAAAGATGAAAAGTGTATGGAAGTATGAACATTTAAGACAATTGTGCCTTTAGCTAATTGGACTTGCTGT
CAAACTTCAGAGTGAATGCCATCCAGATACTTGTACTCAAATGACAGCAACTGAACAATGGATTTTTCTTTGCGCAGCTC
ATAAAACTCCAAAAGAGTGTCCTGCTATAGACTATACTAGACACACACTTGATGGAGCTGCATGTCTTCTGAATAGCAAT
AAATATTTTCCCAGCAGGGTTAGCATAAAGGAATCATCTGTAGTGAAACCAAAATCAGTATGCCATAGGATTTACAGAAT
ATTTTCACATGTTTATTTTCATCATTGGCAGATATTTGATGAATATGAAGATGAAACATTTTTGTGTCATCGGTTTATTA
AATTTTTGATGAAATATAATTTGATGTCCAAGGATAACCTGATTGTACCAATTTTAGAAGAGGAAGTACAGAATTCAATT
TCTGGGGAAAGTGAAGCA

Alignment

ORF - retro_pabe_2021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.6 %
• Parental protein coverage: 85.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDSTLAVQQYIQQNIRADCSNIDKI-LEPPEGQDEGVWKYEHLRQFCLELNGLAVKLQSECHPDTCTQMT
          MDSTLA.QQ.IQQN.RADCSNIDKI.L.........VWKYEHLRQ.CL.L.GLAVKLQSECHPDTCTQMT
Retrocopy MDSTLAAQQSIQQNVRADCSNIDKI<LKHLKAKMKSVWKYEHLRQLCL*LIGLAVKLQSECHPDTCTQMT

Parental  ATEQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSRVSIKESSVAKLGSVCRRIYRIFSHAY
          ATEQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSRVSIKESSV.K..SVC.RIYRIFSH.Y
Retrocopy ATEQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNKYFPSRVSIKESSVVKPKSVCHRIYRIFSHVY

Parental  FHHRQIFDEYENETFLCHRFTKFVMKYNLMSKDNLIVPILEEEVQNSVSGESEA
          FHH.QIFDEYE.ETFLCHRF.KF.MKYNLMSKDNLIVPILEEEVQNS.SGESEA
Retrocopy FHHWQIFDEYEDETFLCHRFIKFLMKYNLMSKDNLIVPILEEEVQNSISGESEA

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	20.96 RPM
SRP007412_cerebellum	0.00 RPM	30.28 RPM
SRP007412_heart	0.00 RPM	19.18 RPM
SRP007412_kidney	0.00 RPM	11.70 RPM
SRP007412_liver	0.00 RPM	11.14 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2021 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2021 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2021 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004020	2 retrocopies	retro_cjac_1960, retro_cjac_3238,
Cavia porcellus	ENSCPOG00000012746	2 retrocopies	retro_cpor_318, retro_cpor_804,
Homo sapiens	ENSG00000115540	2 retrocopies	retro_hsap_2275, retro_hsap_906,
Gorilla gorilla	ENSGGOG00000009005	2 retrocopies	retro_ggor_733, retro_ggor_743,
Latimeria chalumnae	ENSLACG00000015430	1 retrocopy	retro_lcha_112,
Macaca mulatta	ENSMMUG00000016547	1 retrocopy	retro_mmul_829,
Monodelphis domestica	ENSMODG00000012305	2 retrocopies	retro_mdom_1333, retro_mdom_963,
Oryctolagus cuniculus	ENSOCUG00000005712	1 retrocopy	retro_ocun_30,
Otolemur garnettii	ENSOGAG00000000272	1 retrocopy	retro_ogar_2739,
Ochotona princeps	ENSOPRG00000016650	2 retrocopies	retro_opri_444, retro_opri_812,
Pongo abelii	ENSPPYG00000013047	6 retrocopies	retro_pabe_1943, retro_pabe_2021 , retro_pabe_3600, retro_pabe_781, retro_pabe_795, retro_pabe_970,
Sarcophilus harrisii	ENSSHAG00000017821	1 retrocopy	retro_shar_351,
Ictidomys tridecemlineatus	ENSSTOG00000021024	1 retrocopy	retro_itri_727,
Tarsius syrichta	ENSTSYG00000001726	1 retrocopy	retro_tsyr_1673,