RetrogeneDB ID: retro_cfam_1208

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 26:24838183..24838748(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000013339
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPA1
• Ensembl ID: ENSCAFG00000010564
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide A' [Source:HGNC Symbol;Acc:11152]

Sequence

>retro_cfam_1208
AGCAGGATGGTGAAGCTGATGGCTCAGTACACCAAGCCGTGCAGGACCGTGAGCTGGATCTCCAGGGGTATAGAATTCCT
GTCATTGAAAATCTGGGTGCTACCTTAGACCAGTTTGATGCTATTGATTTTTCTGACAACAAAGTCAGGAAACTGGATGG
TTTTCCTTTGTTGAGAAGGCTGAAAACACTATTAGTGAACAACAATAGAATGTGCCGTACCGGTGAGGGACTTGATCAGG
CTCTACCACGTCTGAGAGAACTCATTCTCACCAACAATAGAGTCTTGTGGAACTGGGTGACCTGGACCCTTTGGCATCTC
TCAAATCACTGACTTACCTAAGTATTCTGAGAAATCCTGTAACAAACAAGAAGCATTATAGACTGTATGTAATTTATGAA
GTTCCACAAGTCAGAGTATTAGATTTCCAGAAGGTGAAACTAAAAGAGCCTCAGGAAGCAGAGAAAATGTTCAAGGGCAA
ACGGGGTACACAACTTGCAAAGGATATTGCCAGGAGAAGCAAAACTTTCAGTCCAGGTGCTGGTTTGCCAACTGACAAAA
AGAAA

Alignment

ORF - retro_cfam_1208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.82 %
• Parental protein coverage: 73.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AELIEQAAQYTN-AVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLLVNNN
          .......AQYT..AV.DRELDL.GY.IPVIENLGATLDQFDAIDFSDN..RKLDGFPLLRRLKTLLVNNN
Retrocopy SRMVKLMAQYTK<AVQDRELDLQGYRIPVIENLGATLDQFDAIDFSDNKVRKLDGFPLLRRLKTLLVNNN

Parental  RICRIGEGLDQALPCLTE-LILTNN-SLVELGDLDPLASLKSLTYLSILRNPVTNKKHYRLYVIYKVPQV
          R.CR.GEGLDQALP.L.E.....N..SLVELGDLDPLASLKSLTYLSILRNPVTNKKHYRLYVIY.VPQV
Retrocopy RMCRTGEGLDQALPRLRELILTNNR<SLVELGDLDPLASLKSLTYLSILRNPVTNKKHYRLYVIYEVPQV

Parental  RVLDFQKVKLKERQEAEKMFKGKRGAQLAKDIARRSKTFNPGAGLPTDKKK
          RVLDFQKVKLKE.QEAEKMFKGKRG.QLAKDIARRSKTF.PGAGLPTDKKK
Retrocopy RVLDFQKVKLKEPQEAEKMFKGKRGTQLAKDIARRSKTFSPGAGLPTDKKK

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	0.00 RPM	21.42 RPM
SRP017611_brain	0.00 RPM	10.80 RPM
SRP017611_kidney	0.00 RPM	22.12 RPM
SRP017611_liver	0.00 RPM	13.05 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1208 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1208 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1208 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007128	1 retrocopy	retro_amel_850,
Bos taurus	ENSBTAG00000013593	1 retrocopy	retro_btau_1453,
Canis familiaris	ENSCAFG00000010564	1 retrocopy	retro_cfam_1208 ,
Echinops telfairi	ENSETEG00000010019	1 retrocopy	retro_etel_1366,
Felis catus	ENSFCAG00000018594	1 retrocopy	retro_fcat_322,
Homo sapiens	ENSG00000131876	2 retrocopies	retro_hsap_2148, retro_hsap_2601,
Loxodonta africana	ENSLAFG00000012638	1 retrocopy	retro_lafr_1230,
Myotis lucifugus	ENSMLUG00000014213	1 retrocopy	retro_mluc_2442,
Mustela putorius furo	ENSMPUG00000010938	1 retrocopy	retro_mputfur_1139,
Oryctolagus cuniculus	ENSOCUG00000017417	3 retrocopies	retro_ocun_1248, retro_ocun_1775, retro_ocun_366,
Pan troglodytes	ENSPTRG00000007513	1 retrocopy	retro_ptro_1525,
Tupaia belangeri	ENSTBEG00000001669	2 retrocopies	retro_tbel_1772, retro_tbel_3447,
Tarsius syrichta	ENSTSYG00000003965	2 retrocopies	retro_tsyr_1229, retro_tsyr_1943,