RetrogeneDB ID: retro_cfam_1177

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 25:7684582..7685089(-)
• Located in intron of: ENSCAFG00000006376

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK13
• Ensembl ID: ENSCAFG00000023297
• Aliases: None
• Description: None

Sequence

>retro_cfam_1177
AAAAACACAGCCACAATAATGGAGGAATTGGCAGATGCTCTGACTTACTGCCATGAGAAAAAGGTGATTCACGGGGATAT
TAAACCAGAGAACCTACTGCTCGGGTTCAAGGGTGAGGTGAAAATTGCAGACTTCGGCTGGTCTGTGCACACACCATCTC
TGAGGAGAAAGACAATGTGTGGGACTCCGGACTACTTGCCCCCAGAAATGATTGAGAGGAGAACATACAATGAGAAGGTT
GATCTATGGTGCACTGGAGTACTTTGCTATGAGCTGTTGGTAGGATATCCACCCTTTGAGAGCCCTTCCCATAATGAGAC
CTACAGACGCATCCTCAAGGTAGACCTACGATTTCCCCCATCATTACCTTTGGGGGCCTAGGACTTAGTCTCCAAGCTTC
TCAGATACCAGCCTTTGGAAAGGCTACCCTTGGCCCAGATCATGGAGCACCCCTGGGTCAGGGCCCACTCGAGGAGGGTG
TTGCTTCCATCTGTTCAAATGGCTTCT

Alignment

ORF - retro_cfam_1177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.86 %
• Parental protein coverage: 55.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QHTATIMEELADALTYCHEKKVIHRDIKPENLLLGFKGEVKIADFGWSVHTPSLRRKTMCGTLDYLPPEM
          ..TATIMEELADALTYCHEKKVIH.DIKPENLLLGFKGEVKIADFGWSVHTPSLRRKTMCGT.DYLPPEM
Retrocopy KNTATIMEELADALTYCHEKKVIHGDIKPENLLLGFKGEVKIADFGWSVHTPSLRRKTMCGTPDYLPPEM

Parental  IERRTYNEKVDLWCIGVLCYELLVGYPPFESPSHNETYRRILKVDLRFPPSLPLGAQDLVSKLLRYQPLE
          IERRTYNEKVDLWC.GVLCYELLVGYPPFESPSHNETYRRILKVDLRFPPSLPLGA.DLVSKLLRYQPLE
Retrocopy IERRTYNEKVDLWCTGVLCYELLVGYPPFESPSHNETYRRILKVDLRFPPSLPLGA*DLVSKLLRYQPLE

Parental  RLPLAQIMEHPWVRAHSRRVLPPSVQMAS
          RLPLAQIMEHPWVRAHSRRVL.PSVQMAS
Retrocopy RLPLAQIMEHPWVRAHSRRVLLPSVQMAS

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	0.55 RPM
SRP017611_brain	0.16 RPM	1.03 RPM
SRP017611_kidney	0.07 RPM	0.07 RPM
SRP017611_liver	0.07 RPM	0.15 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1177 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1177 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023297	1 retrocopy	retro_cfam_1177 ,
Canis familiaris	ENSCAFG00000029331	3 retrocopies	retro_cfam_1027, retro_cfam_257, retro_cfam_764,
Echinops telfairi	ENSETEG00000015413	1 retrocopy	retro_etel_1828,
Macropus eugenii	ENSMEUG00000014431	2 retrocopies	retro_meug_741, retro_meug_947,
Mus musculus	ENSMUSG00000070837	1 retrocopy	retro_mmus_2455,
Otolemur garnettii	ENSOGAG00000000999	6 retrocopies	retro_ogar_1122, retro_ogar_1159, retro_ogar_1240, retro_ogar_1293, retro_ogar_2384, retro_ogar_923,