RetrogeneDB ID: retro_cfam_684

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:38330094..38330953(-)
• Located in intron of: ENSCAFG00000006596

Retrocopy information

• Ensembl ID: ENSCAFG00000023676
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NT5C2
• Ensembl ID: ENSCAFG00000010354
• Aliases: None
• Description: 5'-nucleotidase, cytosolic II [Source:HGNC Symbol;Acc:8022]

Sequence

>retro_cfam_684
TCTTTTGGCTTTGAGCTTACTGTGGAGAGATTAGTTTTTTTTGGCTACCCTCAGGAACTGCTCAGCTTTGCTTATGATTC
TACATTCCCTACCAGGGGACTTGTTTTTGATACACTATATGGAAATCTTTTGAAAGTTGATGCATATGGAAATCTTTTGG
TCTGTGCACATGGATTTAACTTCATAAGAGGACCAGAAACTAGAGAGCAGTATCCAAATAAATTTATCCAGCGAGATGAC
ACTGAAAGATTTTACATTTTGAACACAATATTCAACCTACCAGAGACCTACCTGTTGGCCTGCCTTGTAGATTTTTTTAC
TAATTGTCTTAGATATACCAGCTGTGAAACAGGATTTAAAGATGGGGGACCTCTTCATGTCTTACCGAAGTATGTTCCAG
GGTGTAAGAGATGCTGTCGACTGGGTTCATTATAAGGGTTCCCTTAAGGAAAAGACAGTTGAAAATCTTGAGAAGTATGT
AGTCAAAGATGGAAAACTGCCTTTGCTTTTGAGCCGAATGAAAGAAGTAGGGAAAGTGTTTCTTGCCACCAACAGTAACT
ATAAATATACAGATAAAATTATGACTTACCTGTTTGATTTCCCACATGGCCCCAAGCCTGGGAGTTCCCATCGACCATGG
CAGTCCTACTTTGACCTGATTTTGGTGGATGCACAGAAGCCACTCTTTTTTGGAGAAGGCACTGTACTGCATCAGGTGGA
TACTAAAACTGGCAAGCTGAAAATTGGTACCTACACAGGGCCCTTACAGCATGGCATCGTCTACTCAGGAGGTTCATCAG
ATACAGTCTGTGATCTCTTGGGAGCCAAGGGCAAAGATATTTTGTATATTGGAGATCAC

Alignment

ORF - retro_cfam_684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.17 %
• Parental protein coverage: 50.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLGFELTVERLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQ
          S.GFELTVERL...GYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQ
Retrocopy SFGFELTVERLXXXGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGPETREQ

Parental  YPNKFIQRDDTERFYILNTLFNLPETYLLACLVDFFTNCPRYTSCETGFKDG-DLFMSYRSMFQDVRDAV
          YPNKFIQRDDTERFYILNT.FNLPETYLLACLVDFFTNC.RYTSCETGFKDG.DLFMSYRSMFQ.VRDAV
Retrocopy YPNKFIQRDDTERFYILNTIFNLPETYLLACLVDFFTNCLRYTSCETGFKDG>DLFMSYRSMFQGVRDAV

Parental  DWVHYKGSLKEKTVENLEKYVVKDGKLPLLLSRMKEVGKVFLATNSDYKYTDKIMTYLFDFPHGPKPGSS
          DWVHYKGSLKEKTVENLEKYVVKDGKLPLLLSRMKEVGKVFLATNS.YKYTDKIMTYLFDFPHGPKPGSS
Retrocopy DWVHYKGSLKEKTVENLEKYVVKDGKLPLLLSRMKEVGKVFLATNSNYKYTDKIMTYLFDFPHGPKPGSS

Parental  HRPWQSYFDLILVDARKPLFFGEGTVLRQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTVCDLLGAKGKD
          HRPWQSYFDLILVDA.KPLFFGEGTVL.QVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTVCDLLGAKGKD
Retrocopy HRPWQSYFDLILVDAQKPLFFGEGTVLHQVDTKTGKLKIGTYTGPLQHGIVYSGGSSDTVCDLLGAKGKD

Parental  ILYIGDH
          ILYIGDH
Retrocopy ILYIGDH

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	40.28 RPM
SRP017611_brain	0.00 RPM	29.38 RPM
SRP017611_kidney	0.07 RPM	69.87 RPM
SRP017611_liver	0.00 RPM	29.01 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_684 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_684 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_684 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009184	1 retrocopy	retro_cfam_418,
Canis familiaris	ENSCAFG00000010354	1 retrocopy	retro_cfam_684 ,
Choloepus hoffmanni	ENSCHOG00000004098	1 retrocopy	retro_chof_280,
Microcebus murinus	ENSMICG00000012316	1 retrocopy	retro_mmur_1476,
Rattus norvegicus	ENSRNOG00000020179	1 retrocopy	retro_rnor_430,
Tupaia belangeri	ENSTBEG00000017707	4 retrocopies	retro_tbel_2188, retro_tbel_3201, retro_tbel_3465, retro_tbel_3467,