RetrogeneDB ID: retro_ptro_2912

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:103183947..103184583(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR45L
• Ensembl ID: ENSPTRG00000009807
• Aliases: None
• Description: None

Sequence

>retro_ptro_2912
ATGAACCTCTTACTGTGTAACCCCCACTGCAACTGACGGCACTACCCCTGCTTCCACAGGGACCACGGATGCGTATACAT
GGAATGGAAACTGGATTCCGAATCTATAATGCCGATCCATTAAAAAAAAAAAGAAGAAGAAGAGAAAAACAAGAATTCCT
AGAAGAAGGTGTTGGCCATGTTGAAATATTATTTCACAGTAGCTATTTAGCTTGCTTTAGTGGCCGGTGGGGAAAAGCTG
AAAATAGCCTCCCGGTAAAGCGACAATCTGGGATGACCAGAAAAGGACTGTTATTGAAGTAAAAGTTTCTACAGAAGTTA
AGGCGGTCAAATTGTGACAAGATAGAATTGTGGTCGTTTTGGGTTACTTGATTAAGGTATTTACAAGGATATGCAGTGCC
CATCAGTCACACGTCTTGGAAACCTGCTCTAACCTTAAAGGCCTTTGTGCCTTGTGTCCCAGTAGATAGTAACAGCTCTC
TCCTGACCTCCCCCATCACACACATGAGTTATGTGAAGCTTGTGGTCTTGCTAGCACCAAGAAGCCACCTGTAGACCTTC
TTGCACACAAGGACGTCCTAAACTGGTGGCCCTCAACCACCAGTAGGGAACAAGAATTGCAACCACATCTCGAAAG

Alignment

ORF - retro_ptro_2912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.45 %
• Parental protein coverage: 59.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MNLLPCNPHGNGLLYAGFNQDHGCFAC-GMENGFRVYNTDPL----KEKEKQEFLEGGVGHVEMLFRCNY
          MNLL.CNPH.N...Y..F..DHGC....GME.GFR.YN.DP........EKQEFLE.GVGHVE.LF...Y
Retrocopy MNLLLCNPHCN*RHYPCFHRDHGCVYM<GMETGFRIYNADPXXXXXRRREKQEFLEEGVGHVEILFHSSY

Parental  LALVGG--GKKPKYPP-NKVMIWDDLKKKTVIEIEFSTEVKAVKLRRDRIVVVLDSMIKVFTFTHNPHQL
          LA...G..GK.....P..K..IWDD..K.TVIE...STEVKAVKL..DRIVVVL...IKVFT.....HQ.
Retrocopy LACFSGRWGKAENSLP<GKATIWDD-QKRTVIEVKVSTEVKAVKL*QDRIVVVLGYLIKVFTRICSAHQS

Parental  HVFETCYNPKGLCVLCPN-SNNS-LLAFPGTHTGHVQLV-DLASTEKPPVDIPAHEGVLS-CIALNLQ-G
          HV.ETC.N.KGLC.LCP....NS.LL..P.TH...V.LV..LAST.KPPVD..AH..VL....ALN.Q.G
Retrocopy HVLETCSNLKGLCALCPS>DSNSSLLTSPITHMSYVKLV<GLASTKKPPVDLLAHKDVLN<LVALNHQ*G

Parental  TRIATASEK
          TRIAT.S.K
Retrocopy TRIATTSRK

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	75.52 RPM
SRP007412_cerebellum	0.00 RPM	130.92 RPM
SRP007412_heart	0.00 RPM	43.25 RPM
SRP007412_kidney	0.00 RPM	102.91 RPM
SRP007412_liver	0.00 RPM	85.14 RPM
SRP007412_testis	0.00 RPM	108.02 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2912 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2912 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2912 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005657	1 retrocopy	retro_cpor_322,
Homo sapiens	ENSG00000141580	2 retrocopies	retro_hsap_1820, retro_hsap_1879,
Gorilla gorilla	ENSGGOG00000006132	2 retrocopies	retro_ggor_1376, retro_ggor_2173,
Macropus eugenii	ENSMEUG00000013344	1 retrocopy	retro_meug_233,
Macaca mulatta	ENSMMUG00000021803	1 retrocopy	retro_mmul_1330,
Mus musculus	ENSMUSG00000025173	1 retrocopy	retro_mmus_1487,
Nomascus leucogenys	ENSNLEG00000010516	1 retrocopy	retro_nleu_1227,
Pongo abelii	ENSPPYG00000008785	2 retrocopies	retro_pabe_150, retro_pabe_1559,
Pan troglodytes	ENSPTRG00000009807	3 retrocopies	retro_ptro_1171, retro_ptro_1262, retro_ptro_2912 ,
Pteropus vampyrus	ENSPVAG00000006212	1 retrocopy	retro_pvam_158,