RetrogeneDB ID: retro_cfam_1972

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:13039585..13040581(+)
• Located in intron of: ENSCAFG00000011476

Retrocopy information

• Ensembl ID: ENSCAFG00000029003
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000018353
• Aliases: None
• Description: None

Sequence

>retro_cfam_1972
AGATTTTTAAAAAATACAATGTCTAATGGTTATGAAGACCACATGGCCGAAGACTGCAGGGATGATATCGGGAGAACGAA
TTTAATTGTCAACTACCTCCCTCAGAACATGACCCAGGATGAGTTACGGAGTCTGTTCAGCAGTATTGGTGAAGTTGAAT
CTGCAAAACTCATTCGGGATAAAGTAGCAGGGCACAGCCTGGGCTATGGTTTCCTGAACTACGTGACTGCCAAGGACGCA
GAGAGAGCAATCAACACGCTGAATGGCCTGCGGCTCCAGTCAAAAACCATTAAGGTGTCGTATGCTCGCCCGAGCTCAGA
AGTCATCAAAGATGCCAACCTGTACATCAGTGGGCTCCCGCGGACCATGACCCAGAAGGACGTGGAGGATACGTTCTCTC
GGTTCTGGCGAATCATCAACTCCCGGGTCCTGGTGGATCAGACCACAGGTTTGTCCAGAGGGGTTGCGTTTATCCGGTTT
GACAAACGGTCGGAGGCAGAAGAGGCAATTACCAGTTTCAATGGTCATAAACCCCCAGGTTCCTCTGAGCCCATTACAGT
GAAGTTTGCAGCCAACCCCAACCAGAACAAAAACGTGGCACTGCTCTCCCAGCTGTACCACTCGCCTGCCAGACGGTTCG
GAGGCCCTGTTCATCACCAGGCACAGAGATTCAGGTTCTCCCCTATGGGTGTAGATCACATGAGTGGGCTTTCTGGTGTC
AATGTCCCAGGCAACGCGTCTTCGGGCTGGTGCATCTTCATCTACAACCTCGGGCAGGACGCCGATGAGGGGATCCTCTG
GCAGATGTTTGGCCCCTTTGGGGCAGTCACCAATGTCAAAGTGATTCGCGACTTCAACACCAACAAGTGCAAAGGCTTTG
GCTTTGTGACCATGACAAACTATGAAGAAGCCGCCATGGCCATAGCAAGTCTGAACGGCTACCGCCTGGGGGACAAAATC
TTACAGGTTTCCTTCAAAACCAACAAGTCCCACAAA

Alignment

ORF - retro_cfam_1972 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.1 %
• Parental protein coverage: 99.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFLKNTMSNGYEDHMAEDCRDDIGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYG
          RFLKNTMSNGYEDHMAEDCRDDIGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYG
Retrocopy RFLKNTMSNGYEDHMAEDCRDDIGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYG

Parental  FVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIIN
          F.NYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVED.FSRF.RIIN
Retrocopy FLNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDTFSRFWRIIN

Parental  SRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFAANPNQNKNVALLSQLYHSPA
          SRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFAANPNQNKNVALLSQLYHSPA
Retrocopy SRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFAANPNQNKNVALLSQLYHSPA

Parental  RRFGGPVHHQAQRFRFSPMGVDHMSGLSGVNVPGNASSGWCIFIYNLGQDADEGILWQMFGPFGAVTNVK
          RRFGGPVHHQAQRFRFSPMGVDHMSGLSGVNVPGNASSGWCIFIYNLGQDADEGILWQMFGPFGAVTNVK
Retrocopy RRFGGPVHHQAQRFRFSPMGVDHMSGLSGVNVPGNASSGWCIFIYNLGQDADEGILWQMFGPFGAVTNVK

Parental  VIRDFNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSFKTNKSHK
          VIRDFNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSFKTNKSHK
Retrocopy VIRDFNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSFKTNKSHK

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	0.88 RPM	9.91 RPM
SRP017611_brain	0.71 RPM	9.61 RPM
SRP017611_kidney	0.86 RPM	12.22 RPM
SRP017611_liver	0.22 RPM	5.08 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cfam_1972 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BI397434	13040285	13040407	97.5	115	3	112

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1972 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003081	2 retrocopies	retro_cfam_45, retro_cfam_837,
Canis familiaris	ENSCAFG00000018353	1 retrocopy	retro_cfam_1972 ,
Choloepus hoffmanni	ENSCHOG00000006810	2 retrocopies	retro_chof_2564, retro_chof_44,
Tupaia belangeri	ENSTBEG00000015038	1 retrocopy	retro_tbel_3670,