RetrogeneDB ID: retro_pabe_2420

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3_random:16696803..16697487(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFC3
• Ensembl ID: ENSPPYG00000005272
• Aliases: None
• Description: replication factor C (activator 1) 3, 38kDa [Source:HGNC Symbol;Acc:9971]

Sequence

>retro_pabe_2420
ATGAGCCTCTGGGTGGACAAGTACCAGCCCTAATCCTTGGGATGGATGGAGTATCATAGGGAGCAGGCAGCCCAGCTGTA
CAACCTGGTGCAGGGTGGTGAGTTTCCTCACCTTTAAGTGTATGGACCATCAGGTGCTGGAAAAAAGACAAATGCATGTG
TGTGTTCTACATGAACTTTATGGTGTTGGAGTGGAAAAATTGAGAATTAAATATCAGACCATCAGGACTCCATCTAAAAA
AATTGAAATTAGCACCATTGCAAGTAATTACCACCTTGAAGTTAATCCCAGTGATGCTGGAAATATTGATGAGGTAGTAA
TTCAGAAGATGTCGAAAACAGTGGCTCAGTCACAGTAACTTGAAACAAACTGTCAGATATTTTAAAATGGTATTATTGAC
AGAAGGTTGACAAACTTATTAAAGATGCTCAACATGCCTTGTAAAGAATCATGGAAAAGTATATGTCCACCTGCAGATTG
GTCTTGTGCTACAGTTCTACATCTAATGTGATACCACCTATTTGTAGTAGGTGCTTGGCAGTTTGTGTGCCTGCTCCCAG
CACTGGAGATATTTACCGTGTGTTATGTACTGTGTACAAGAAGGAAGATCTGAATCTTCCTTCACAACTGACTCATAGAC
TTGCAGAGAAGTCCTGCAGAAATCTCACGAAAGCCCTGCTTATG

Alignment

ORF - retro_pabe_2420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.46 %
• Parental protein coverage: 64.33 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSLWVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVYGPSGAGKKTRI-MCILRELYGVGVEKLRI
          MSLWVDKY.P.SLG...YH.EQAAQL.NLVQ.G.FPHL.VYGPSGAGKKT....C.L.ELYGVGVEKLRI
Retrocopy MSLWVDKYQP*SLGWMEYHREQAAQLYNLVQGGEFPHL*VYGPSGAGKKTNA>VCVLHELYGVGVEKLRI

Parental  EHQTITTPSKKKIEISTIASNYHLEVNPSDAGNSDRVVVQEMLKTVAQSQQLETNSQRDFKVVLLTEVDK
          ..QTI.TPS.KKIEISTIASNYHLEVNPSDAGN.D.VV.Q.M.KTVAQSQ.LETN.Q.............
Retrocopy KYQTIRTPS-KKIEISTIASNYHLEVNPSDAGNIDEVVIQKMSKTVAQSQ*LETNCQIF*NGIIDRRLTN

Parental  LTK-DAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLP
          L.K.DAQHAL.R.MEKYMSTCRL.LC..STS.VIPPI.SRCLAV.VPAPS..DI..VL.TV.KKE.LNLP
Retrocopy LLK<DAQHAL*RIMEKYMSTCRLVLCYSSTSNVIPPICSRCLAVCVPAPSTGDIYRVLCTVYKKEDLNLP

Parental  SQLAHRLAEKSCRNLRKALLM
          SQL.HRLAEKSCRNL.KALLM
Retrocopy SQLTHRLAEKSCRNLTKALLM

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	2.60 RPM
SRP007412_cerebellum	0.00 RPM	10.21 RPM
SRP007412_heart	0.00 RPM	2.08 RPM
SRP007412_kidney	0.00 RPM	1.69 RPM
SRP007412_liver	0.00 RPM	1.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2420 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2420 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2420 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018380	1 retrocopy	retro_cjac_1611,
Cavia porcellus	ENSCPOG00000008739	1 retrocopy	retro_cpor_405,
Myotis lucifugus	ENSMLUG00000014088	1 retrocopy	retro_mluc_1754,
Mustela putorius furo	ENSMPUG00000001885	1 retrocopy	retro_mputfur_1073,
Nomascus leucogenys	ENSNLEG00000001169	1 retrocopy	retro_nleu_674,
Pongo abelii	ENSPPYG00000005272	1 retrocopy	retro_pabe_2420 ,
Tupaia belangeri	ENSTBEG00000004725	1 retrocopy	retro_tbel_4191,
Tarsius syrichta	ENSTSYG00000009501	2 retrocopies	retro_tsyr_1772, retro_tsyr_331,