RetrogeneDB ID: retro_cfam_1694

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:37656405..37657366(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008369
• Aliases: None
• Description: None

Sequence

>retro_cfam_1694
GAAGAAATCAATAATTTCAAGACACCAAGCAAATTATTGGAAAAAAGAAATCTGCATTATGTTCAACTCCATGTATAAAT
ATTCTTGCCTCTCCATTTATGCAGAAGCTTGACTTTGGTACTGGGGTAAATGTGTACCTTATGAAAAGATCTCCAAGAGG
TTTGTCTCATTCTCCTTGGGCTATGAAAAAGATTAACCCTAAATGTAATGATCATTATCAAAGTATGTATCAAAAGAGAT
TAATAGATGAAGCTAAGATTTTGAAAAACCTCCATCACCCAAACATTGTAGGTTATCGTGCCTAAACTGAAGCCAGTGAT
GGTAGTCTATGTCTTGCTATGGAATATGGAGGTGAAAAGTCTCTAAATGACTTAATAGAAGAACGAAATAAAGACAGCCA
AGATCCTTTTCCAGCAGCCATAATTTTAAAAGTTGCTTTGAACATGGCAAGAGGGTTAAAGTATGTACACCAAGAAAAGA
AACTGCTTCATGGAGACATAAAGTCTTCAAATGTTGTAATTAAAGGTGATTTTGAAACAATTAAAATCTGTGATGTAGGA
GTCTCTCTGCCACTTGATGAAAATATGACTGTGACTGATCCTGAGGCCTGTTATATTGGCACTGAGCCTTGGAAACCCAA
GGAAGCTTTGGAAGAGAATGGCATTATTACTGACAAGGCAGACATATTTGCTTTTGGCCTGACTCTGTGGGAAATGATGA
CTTTGTCTATTCCACACATTAATCTTCCAGATGATGATGATGATGAAGATAAAACTTTTGATGAAAGCGACTTTGATGAT
GAAGCATACTATGCAGTTTGGGGACGAGGCCACCTGTTAATATGGAAGAACTGGATGAAACGTACCAGAAAGTAATTGAA
CTTTTCTCTGTATGCACTAACAAAGATCCTAAAGATTGTCCTTCTGCCGCACACATCGTGGAAGCTTTGGAAATAGATGT
C

Alignment

ORF - retro_cfam_1694 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.3 %
• Parental protein coverage: 99.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEINNFKTPSKLSEK-KKSALCSTPCINIPASPFMQKLGFGTGVNVYLMKRSPRGLSHSPWAVKKINPKC
          EEINNFKTPSKL.EK.KKSALCSTPCINI.ASPFMQKL.FGTGVNVYLMKRSPRGLSHSPWA.KKINPKC
Retrocopy EEINNFKTPSKLLEK<KKSALCSTPCINILASPFMQKLDFGTGVNVYLMKRSPRGLSHSPWAMKKINPKC

Parental  NDHYQSMYQKRLIDEAKILKNLHHPNIVGYRAFTEASDGSLCLAMEYGGEKSLNDLIEERNKDSQDPFPA
          NDHYQSMYQKRLIDEAKILKNLHHPNIVGYRA.TEASDGSLCLAMEYGGEKSLNDLIEERNKDSQDPFPA
Retrocopy NDHYQSMYQKRLIDEAKILKNLHHPNIVGYRA*TEASDGSLCLAMEYGGEKSLNDLIEERNKDSQDPFPA

Parental  AIILKVALNMARGLKYLHQEKKLLHGDIKSSNVVIKGDFETIKICDVGVSLPLDENMTVTDPEACYIGTE
          AIILKVALNMARGLKY.HQEKKLLHGDIKSSNVVIKGDFETIKICDVGVSLPLDENMTVTDPEACYIGTE
Retrocopy AIILKVALNMARGLKYVHQEKKLLHGDIKSSNVVIKGDFETIKICDVGVSLPLDENMTVTDPEACYIGTE

Parental  PWKPKEALEENGIITDKADIFAFGLTLWEMMTLSIPHINLPDDDDDDEDKTFDESDFDDEAYYA-ALGTR
          PWKPKEALEENGIITDKADIFAFGLTLWEMMTLSIPHINLPDDDDD.EDKTFDESDFDDEAYYA..LGTR
Retrocopy PWKPKEALEENGIITDKADIFAFGLTLWEMMTLSIPHINLPDDDDD-EDKTFDESDFDDEAYYA<SLGTR

Parental  PPVNMEELDETYQKVIELFSVCTNEDPKDRPSAAHIVEALEIDV
          PPVNMEELDETYQKVIELFSVCTN.DPKD.PSAAHIVEALEIDV
Retrocopy PPVNMEELDETYQKVIELFSVCTNKDPKDCPSAAHIVEALEIDV

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	1.68 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.26 RPM
SRP017611_liver	0.00 RPM	0.07 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1694 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1694 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1694 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021069	1 retrocopy	retro_btau_150,
Canis familiaris	ENSCAFG00000008369	1 retrocopy	retro_cfam_1694 ,
Dipodomys ordii	ENSDORG00000014896	1 retrocopy	retro_dord_697,
Myotis lucifugus	ENSMLUG00000009596	1 retrocopy	retro_mluc_713,
Monodelphis domestica	ENSMODG00000015986	1 retrocopy	retro_mdom_245,
Mus musculus	ENSMUSG00000022033	1 retrocopy	retro_mmus_2452,
Otolemur garnettii	ENSOGAG00000009887	1 retrocopy	retro_ogar_3495,
Tupaia belangeri	ENSTBEG00000002239	1 retrocopy	retro_tbel_3290,