RetrogeneDB ID: retro_cfam_944

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:65226458..65226801(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000017228
• Aliases: None
• Description: None

Sequence

>retro_cfam_944
ATGGAGTTGACTAGTGGGACTGCTGAGCCGGTTTCCAGGGAACTGGTGTCTGTGGCACATGCTCTTTCTCTCCTTGCCAG
GTTTTACTTCAACGATCCTGATATTGAGATGGCTTGGGCATCTCAAAGCAATGCAGCATGCTGACATCAGCTATAAGCTG
ATTTCATCAGTTGACTCACAGTTCCTGAAACTCACCAGAGTAGATGACCAAATCTATTCCAAGTTTTGAGAAAATTTTGA
GAAACTCAGGATCAATGGGTTGGACTCAGAAGAGCTCAAATCAGAATCAGTTAAAGAGAAGTGGAGGCCATTCTGTGTGA
CGTTTGACAGAATTGTAGAAGAC

Alignment

ORF - retro_cfam_944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.39 %
• Parental protein coverage: 51.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  METTRGTAEPVPGELVSVAHALSLPAESYGNDPDIEMAWA-MKAMQHAEVYYKLISSVDPQFLKLTKVDD
          ME.T.GTAEPV..ELVSVAHALSL.A..Y.NDPDIEMAWA..KAMQHA...YKLISSVD.QFLKLT.VDD
Retrocopy MELTSGTAEPVSRELVSVAHALSLLARFYFNDPDIEMAWA>LKAMQHADISYKLISSVDSQFLKLTRVDD

Parental  QIYSEFRKNFEKLRIDVLDPEELKSESAKEKWRPFCLKFDGVVED
          QIYS.F..NFEKLRI..LD.EELKSES.KEKWRPFC..FD..VED
Retrocopy QIYSKF*ENFEKLRINGLDSEELKSESVKEKWRPFCVTFDRIVED

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	32.89 RPM
SRP017611_brain	0.16 RPM	23.26 RPM
SRP017611_kidney	0.00 RPM	107.24 RPM
SRP017611_liver	0.00 RPM	10.15 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_944 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_944 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_944 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017228	2 retrocopies	retro_cfam_1588, retro_cfam_944 ,
Callithrix jacchus	ENSCJAG00000018571	1 retrocopy	retro_cjac_1880,
Equus caballus	ENSECAG00000009882	1 retrocopy	retro_ecab_532,
Erinaceus europaeus	ENSEEUG00000001116	1 retrocopy	retro_eeur_377,
Monodelphis domestica	ENSMODG00000009685	2 retrocopies	retro_mdom_1002, retro_mdom_572,
Mus musculus	ENSMUSG00000031226	1 retrocopy	retro_mmus_1569,
Oryctolagus cuniculus	ENSOCUG00000001088	3 retrocopies	retro_ocun_1017, retro_ocun_1402, retro_ocun_595,
Otolemur garnettii	ENSOGAG00000015205	1 retrocopy	retro_ogar_3063,
Rattus norvegicus	ENSRNOG00000002662	3 retrocopies	retro_rnor_1703, retro_rnor_1705, retro_rnor_826,
Sarcophilus harrisii	ENSSHAG00000017872	1 retrocopy	retro_shar_132,
Tupaia belangeri	ENSTBEG00000003411	3 retrocopies	retro_tbel_3448, retro_tbel_494, retro_tbel_979,