RetrogeneDB ID: retro_cfam_295

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:23498212..23498896(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPSNAP3A
• Ensembl ID: ENSCAFG00000023949
• Aliases: None
• Description: nipsnap homolog 3A (C. elegans) [Source:HGNC Symbol;Acc:23619]

Sequence

>retro_cfam_295
CCTCAGATGTGTCCGCCTTTGCTATGGAGGGCGGGGGGCAGACAGTATGATGGAATACTCCGTGAGTTTCATACTTACGG
CCTTAAACTTTTAAAGATAAATGAGTTTCCAGAAAATGTTACAAAAATCATTCATCTTTGAACAGCTGACTCTGCATTGG
TTGGTTTCAGGAGTGCAAAATTTGGAGGCAGAGTAAATGAAGTGTTTCATGTTTGGAAGTGTGATGGTTTTGCTCATGAA
ACTGAAGTTCAGAAAGGCTTGATCAAAAATAAGGAATGCCCAGAACAATTTCTCATCCCAAATTTGGCTCTCCTTGCTAA
CCAAGAGTTTGAGATTACTTACGTGGTACCATTGTCCAAAACAGAAAAGCCTCCAAAGGAGTCCATGAACTGGTTATTTT
CCAGATGAAACCTGATGGGCCAGCTCCGCGGGGTGACACATTAAGAGGGAAGTCACTGCCCTTTAGATTGAAGACACATA
AAACCAACTGGTGTTCTCTGCCCAGAATATGGAGCAACCAGCAGAGCTCGTGTTCTTTGGTGCAATGAGTGTGGATAGTC
GTGTAGCTGGGAGACATCAGTTTCATGAGAACCTCAGACTCATGGTGGCTGTTTGGGAAAATGTCAACTACGAAGTGTTA
CAGCAGAAGAAGCTTTGGATTCCTATGTCACCTCACCGCTGAAA

Alignment

ORF - retro_cfam_295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.36 %
• Parental protein coverage: 92.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PQLCSS--FATGPRQYDGTFYEFRTYCLKPSKMNEFLENVKKNIHLRTAQSELVGFWSVEFGGQMNKVFH
          PQ.C.......G.RQYDG...EF.TY.LK..K.NEF.ENV.K.IHL.TA.S.LVGF.S..FGG..N.VFH
Retrocopy PQMCPPLLWRAGGRQYDGILREFHTYGLKLLKINEFPENVTKIIHL*TADSALVGFRSAKFGGRVNEVFH

Parental  IWKYDNFAHRTEVRKAVAKNKEWQQQCVIPNLALIDEQETEITYLVPWCKLE-KPTKEGVYELVIFQLKP
          .WK.D.FAH.TEV.K...KNKE...Q..IPNLAL...QE.EITY.VP..K.E.K..K.GV.ELVIFQ.KP
Retrocopy VWKCDGFAHETEVQKGLIKNKECPEQFLIPNLALLANQEFEITYVVPLSKTE<KASK-GVHELVIFQMKP

Parental  GGPALWGDAF-KRAINA-HVDLGYSKLVGVFHTEYGALNRVHVLWWNE-SADSRAAGRHQSHEDPRVVAA
          .GPA..GD...KR...A...D....K..GV...EYGA..R..VL.W...S.DSR.AGRHQ.HE..R...A
Retrocopy DGPAPRGDTL<KREVTA<PLD*RHIKPTGVLCPEYGATSRARVL-WCN>SVDSRVAGRHQFHENLRLMVA

Parental  VRESVNYLVSQQNMLLIPTS-FSPLK
          V.E.VNY.V.QQ..L.IP.S..SPLK
Retrocopy VWENVNYEVLQQKKLWIPMS<TSPLK

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	26.42 RPM
SRP017611_brain	0.16 RPM	15.64 RPM
SRP017611_kidney	0.00 RPM	25.03 RPM
SRP017611_liver	0.00 RPM	29.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_295 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_295 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_295 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_978

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014253	1 retrocopy	retro_acar_133,
Canis familiaris	ENSCAFG00000023949	1 retrocopy	retro_cfam_295 ,
Cavia porcellus	ENSCPOG00000009373	1 retrocopy	retro_cpor_690,
Dasypus novemcinctus	ENSDNOG00000000943	1 retrocopy	retro_dnov_482,
Echinops telfairi	ENSETEG00000016120	1 retrocopy	retro_etel_1335,
Myotis lucifugus	ENSMLUG00000010147	1 retrocopy	retro_mluc_924,
Oryctolagus cuniculus	ENSOCUG00000007880	1 retrocopy	retro_ocun_1385,
Tursiops truncatus	ENSTTRG00000012307	1 retrocopy	retro_ttru_1702,