RetrogeneDB ID: retro_cfam_334

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:105458065..105458608(-)
• Located in intron of: ENSCAFG00000023981

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R8
• Ensembl ID: ENSCAFG00000012023
• Aliases: None
• Description: protein phosphatase 1, regulatory subunit 8 [Source:HGNC Symbol;Acc:9296]

Sequence

>retro_cfam_334
CAAATGAATAACCCAGAACTTGAGAAAGATGGCCTCCTGAATGACTTCTCTGAGGCTGTGAAGGATTTCTAGGCTGTGCA
GGGAACGGATCTGGAAAAGAAAAGAAGAGTATAGCCAGAGTGAGAGGTGAATCTCCTCTCTCTGCAGAGGAGAGGCAAAG
AGAGAGCAGCTCCCCTTGTTTGATGGCCACAGGAGTGGGACCAGACACAGAGAGCCAGGAGAATGAGGTGGGTCATCACG
GAGCAGGATCGGAATTTATTAAAGAGTGAGAAAAGGCAATTTGGCAGCTGCATACTGACATTCTGGATGCCCATCAGATG
TTTAAAGATCTGGCCATGATGATCCATGACCAAGATGACCCAATTGACAGCATGCATAGAAAAGCCAATGTGGAAAGCTC
AAAGGTGCTTGCAGACAGAGCCACTGGTCAGTTACAGCAAGCTGCTTTACTATCAGAAAAAAAAAAAAATCTCACAAAAC
ATCTGTATTCTGGTGCTTCTCCTGTTTGTGATTACCGTAATCTTGGTACTTATCTGGCAAATT

Alignment

ORF - retro_cfam_334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.57 %
• Parental protein coverage: 64.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EQRQQKLQKERLMNDFSAALNNFQAVQRRVSEK-EKESIARARAGSRLSAEERQRE-EQLVSFDGHEEWN
          ......L.K..L.NDFS.A...F.AVQ....EK.EK.SIAR.R..S.LSAEERQRE.EQL..FDGH....
Retrocopy QMNNPELEKDGLLNDFSEAVKDF*AVQGTDLEK<EKKSIARVRGESPLSAEERQRE<EQLPLFDGHRSGT

Parental  Q-MQSQEDEVA-ITEQDL-ELIKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSI--EANVESSE
          ....SQE.EV..ITEQD..E.IKE.E.AI.QL..DILD..Q.FKDLAMMIHDQ.D.IDS....ANVESS.
Retrocopy R>TESQENEVG>ITEQDR<EFIKE*EKAIWQLHTDILDAHQMFKDLAMMIHDQDDPIDSMHRKANVESSK

Parental  VHVERATDQLQRAA-YYQ--KKSRKKICILVLVLSVIIVILVFIIWQI
          V...RAT.QLQ.AA.YYQ........ICILVL.L.VI.VILV..IWQI
Retrocopy VLADRATGQLQQAA>YYQXXXXXSQNICILVLLLFVITVILV-LIWQI

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
SRP012049_cerebellum	0.04 RPM	86.43 RPM
SRP017611_brain	0.08 RPM	63.20 RPM
SRP017611_kidney	0.00 RPM	35.66 RPM
SRP017611_liver	0.15 RPM	13.63 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_334 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_334 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_334 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
Canis familiaris	ENSCAFG00000005180	1 retrocopy	retro_cfam_24,
Canis familiaris	ENSCAFG00000012023	1 retrocopy	retro_cfam_334 ,
Homo sapiens	ENSG00000117751	1 retrocopy	retro_hsap_380,
Gorilla gorilla	ENSGGOG00000012062	1 retrocopy	retro_ggor_387,
Loxodonta africana	ENSLAFG00000017834	1 retrocopy	retro_lafr_1173,
Macaca mulatta	ENSMMUG00000006933	1 retrocopy	retro_mmul_491,
Pan troglodytes	ENSPTRG00000000417	1 retrocopy	retro_ptro_296,
Ictidomys tridecemlineatus	ENSSTOG00000004381	2 retrocopies	retro_itri_1611, retro_itri_1704,