RetrogeneDB ID: retro_cfam_1012

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:24138246..24138649(+)
• Located in intron of: ENSCAFG00000005549

Retrocopy information

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

Parental gene information

• Parental gene symbol: CISD2
• Ensembl ID: ENSCAFG00000010779
• Aliases: None
• Description: None

Sequence

>retro_cfam_1012
ATGGTGCTGGAGAGCGTGGCCCGCATCGTGAAGGTGCAGCTCCCAGCGTATCTTAAGCGGCTCCCTGTGCCCTAGAGCAT
TACCGGGTTCGCCCGGCTCACAGTTTCAGAATGGCTTTGATTACTGCCTTTCCTCAGTGTACTTGCACTACTTGGCTACC
TTGCAATGTCCATTCCTCCCGAAGAAAAAACCACAGAAGGATAGCTTGATTAATTTTAAAATACAAAAGGAAAATCCCAA
AGTGGTGAATGAAATAAACATTGAAGATTTGTGTCTCACTAAAGCAGCTTACTGTAGGTGTTGGCGTTCTAAGACGTTTC
CTGCCTGTGATGGTTCACATAATAAACACAATGAATTGACAGGAGATAATGTGGGCCCATTAATACTGAAGAAGAAAGAA
GTA

Alignment

ORF - retro_cfam_1012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVLESVARIVKVQLPAYLKRLPVPESITGFARLTVSEWLRLLPFLGVLALLGYLAIRPFLPKKK-QQKDS
          MVLESVARIVKVQLPAYLKRLPVP.SITGFARLTVSEWL.LLPFL.VLALLGYLA.....P..K..QKDS
Retrocopy MVLESVARIVKVQLPAYLKRLPVP*SITGFARLTVSEWL*LLPFLSVLALLGYLAM-SIPPEEK>PQKDS

Parental  LINLKIQKENPKVVNEINIEDLCLTKAAYCRCWRSKTFPACDGSHNKHNELTGDNVGPLILKKKEV
          LIN.KIQKENPKVVNEINIEDLCLTKAAYCRCWRSKTFPACDGSHNKHNELTGDNVGPLILKKKEV
Retrocopy LINFKIQKENPKVVNEINIEDLCLTKAAYCRCWRSKTFPACDGSHNKHNELTGDNVGPLILKKKEV

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	12.52 RPM
SRP017611_brain	0.00 RPM	6.35 RPM
SRP017611_kidney	0.00 RPM	29.06 RPM
SRP017611_liver	0.00 RPM	5.08 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1012 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1012 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010779	1 retrocopy	retro_cfam_1012 ,
Callithrix jacchus	ENSCJAG00000015530	1 retrocopy	retro_cjac_2668,
Felis catus	ENSFCAG00000028054	1 retrocopy	retro_fcat_1979,
Mus musculus	ENSMUSG00000028165	1 retrocopy	retro_mmus_2257,
Nomascus leucogenys	ENSNLEG00000026930	1 retrocopy	retro_nleu_1331,
Oryctolagus cuniculus	ENSOCUG00000013943	1 retrocopy	retro_ocun_1444,
Ictidomys tridecemlineatus	ENSSTOG00000001408	1 retrocopy	retro_itri_869,