RetrogeneDB ID: retro_cfam_1937

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:8492945..8493800(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSL1D1
• Ensembl ID: ENSCAFG00000018865
• Aliases: None
• Description: ribosomal L1 domain containing 1 [Source:HGNC Symbol;Acc:24534]

Sequence

>retro_cfam_1937
ATGGAGGGTTGAGCTTCCACCACACTGTCATCCTCAGCCGCAGCCTCAGCCTCTGCCCCAGCTACCCTGGCCTGCCTGGG
GCAGCTGGACAAAGGGCAGATTAGAAAAGTGGTGGAAGCTCTGTTGGCACACTCCAGGTCCAGGAAGAACGCAAATGGAT
TGCTTTTGAATGAGAATGAAAATCTCTTTTTAATGGTAGTATTATGGAAGATTCCAAGTAAAGAACTGAGGGTCAGACTG
CCCTTGCTTCATGGTATTCGATCAGATTTAACAGATACTTGTTTACTTCCTCAGGATGAACCCAATTTAACTCCTGAAAA
GACAGAACGGTTTTACAAGAAGCTTTTGAACAAGCATGGAATTAAAACTGTTTCTTAGATTATCCCCCTCCGAACTCTAA
AAAAGGCATATAAAGCTTATGAAGCCAAGCTGTGCCTCTTGGGCAGTTTTGACTTCTTCCTTACTGATGCGAGAATCAGG
TGGCTCTTACCGTCACACCTCGGGAGACATTTCTACCACGGAAAGAACATGCTGGTACCTCTGAACCTTCTGGCCAAGAA
TGTATCCAGGGAGATTAATGAATGCATAGGTAGCACTGTCTTAAACATCTCTAAAAGTGGTTCTTGCAATACTATCCACG
CTGGCCACACTGGAATGGAGGTTGAACACATCATTGATAACATCATCTCTGTGACAAAGAGGCTTTCACAAAAGTTGCCA
GAGAAGTGGGAGAGCATGAAACTCTTTTATGTGAAGACGGAGACGTAGGCCTCCTTGCCCGTCTTTTCCTCACTTGTCAG
CTGTCAGGATGAAGCCAAGGGAATATGCACTCCTAGTCAGAAGAAAAAGGAAGCA

Alignment

ORF - retro_cfam_1937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 58.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGSAPPSPSSSTAASASAPETPACLEQLDKGQIRKAVEALLAHSRSRKNANGLLLNENENFFLMVILWK
          MEG.A....SSS.AASASAP.T.ACL.QLDKGQIRK.VEALLAHSRSRKNANGLLLNENEN.FLMV.LWK
Retrocopy MEG*ASTTLSSSAAASASAPATLACLGQLDKGQIRKVVEALLAHSRSRKNANGLLLNENENLFLMVVLWK

Parental  IPSKELRVRLALPHGIRSDLTDICLLTKDEPNLTPENTERFYKKLLNKHGIKTISQIIPLRTLKKEYKAY
          IPSKELRVRL.L.HGIRSDLTD.CLL..DEPNLTPE.TERFYKKLLNKHGIKT.S.IIPLRTLKK.YKAY
Retrocopy IPSKELRVRLPLLHGIRSDLTDTCLLPQDEPNLTPEKTERFYKKLLNKHGIKTVS*IIPLRTLKKAYKAY

Parental  EAKLRLLGSFDFFLTDARIRRLLPSHLGRHFYHRKKVPVPVNLLAKNLSREINECIGGTVLNISKSGSCS
          EAKL.LLGSFDFFLTDARIR.LLPSHLGRHFYH.K...VP.NLLAKN.SREINECIG.TVLNISKSGSC.
Retrocopy EAKLCLLGSFDFFLTDARIRWLLPSHLGRHFYHGKNMLVPLNLLAKNVSREINECIGSTVLNISKSGSCN

Parental  TIRVGHTGMEVEHIVDNIIAVAKRLSQKLPEKWESVKLLYVKTERSASLPIFSSFVSCQDEAKGICTRIQ
          TI..GHTGMEVEHI.DNII.V.KRLSQKLPEKWES.KL.YVKTE..ASLP.FSS.VSCQDEAKGICT..Q
Retrocopy TIHAGHTGMEVEHIIDNIISVTKRLSQKLPEKWESMKLFYVKTET*ASLPVFSSLVSCQDEAKGICTPSQ

Parental  RKKEA
          .KKEA
Retrocopy KKKEA

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	36.54 RPM
SRP017611_brain	0.00 RPM	28.90 RPM
SRP017611_kidney	0.00 RPM	18.23 RPM
SRP017611_liver	0.00 RPM	29.30 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1937 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1937 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1937 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
Canis familiaris	ENSCAFG00000018865	2 retrocopies	retro_cfam_1937 , retro_cfam_691,
Choloepus hoffmanni	ENSCHOG00000010827	2 retrocopies	retro_chof_1617, retro_chof_852,
Callithrix jacchus	ENSCJAG00000008375	1 retrocopy	retro_cjac_2154,
Cavia porcellus	ENSCPOG00000010630	3 retrocopies	retro_cpor_1262, retro_cpor_276, retro_cpor_822,
Loxodonta africana	ENSLAFG00000013664	1 retrocopy	retro_lafr_364,
Myotis lucifugus	ENSMLUG00000000784	1 retrocopy	retro_mluc_1309,
Monodelphis domestica	ENSMODG00000029494	2 retrocopies	retro_mdom_1240, retro_mdom_573,
Otolemur garnettii	ENSOGAG00000015151	1 retrocopy	retro_ogar_2604,
Rattus norvegicus	ENSRNOG00000048608	1 retrocopy	retro_rnor_2771,
Sarcophilus harrisii	ENSSHAG00000016705	1 retrocopy	retro_shar_836,