RetrogeneDB ID: retro_cfam_1594

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 36:5036489..5037348(-)
• Located in intron of: ENSCAFG00000009375

Retrocopy information

• Ensembl ID: ENSCAFG00000009377
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EXTL2
• Ensembl ID: ENSCAFG00000020002
• Aliases: None
• Description: exostosin-like glycosyltransferase 2 [Source:HGNC Symbol;Acc:3516]

Sequence

>retro_cfam_1594
ATGAAGTATTACCACATCTGCAAACTTCCCGGACGAGTGATGGGCATTGGAGTCCTTCGTTTCTCTCTGGTGGTCATCCT
CGCGCTGCTGCTCGTTTGACCACTTTACTTCCAAATATCAAGGAAGACAAGATGCTTACTTTGCGTAGGGAAATAAAATC
CCAGGGCAAGTCCACTCTGTATTCCTTTACTCTAATAATGCAGACATACAACAGAACAGATCTCTTACTGAGACTCTTAA
ATCATTATCAGGCTGTGCCATATCTGCATAAAGTGATTGTAATGTGGAACAATGTTGGGGAGAAGGGACCAGACGAGTTA
TGGAATTCTCTAGGGCCGCATCCTGTCCCTGTGATCTTCAAACTACAGACAACAAACAGGATAAGAAATCGACTCCAGGT
CTTTCCTGAACTAGAAACCAATGCAGTGTTATGGTAGACGATGACACGCTAATTAGCACCCAAGACCTTGTTTTTGCTTT
CTCAGTTTGGCAGCAATTTCCTGATCAAATTGTAGGATTTGTTCCTAGAAAGCATGTCTCTACTTCATCAGGCATCTACA
GTTATGGAGGTTTTGAACTGCAAACCCCGGGGTTTGGAAATGGTGACCGGTACTCTATGGTGCTGATTGGAGCCTCGTTC
TTCAATAGCAAATACCTTGACCTGTTTCAGAGGCAGCCTGCTGCTCTCCATGCTTTGATAGATGAAATCCAAAACTGTGA
TGATATTGCCATGAATTTTATCATTGCCAAGCACACCGGGAAGACTTCAGGGGTATTTGTGGAACCTGTAAACATGGGCA
ATTTAGAAAAAGAATCCAGTGGTGGCTATCCTGGAATGTGGCATCGAGCTGAGCACTTT

Alignment

ORF - retro_cfam_1594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.12 %
• Parental protein coverage: 87.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRYCHICKLPGRVMGIRVLRFSLVVILVLLLV-AGALTTLLPNIKEDKMLTLRREIKSQGKSTLDSFTLI
          M.Y.HICKLPGRVMGI.VLRFS.....V.L...A..LTTLLPNIKEDKMLTLRREIKSQGKSTL.SFTLI
Retrocopy MKYYHICKLPGRVMGIGVLRFS---LVVILAL<AARLTTLLPNIKEDKMLTLRREIKSQGKSTLYSFTLI

Parental  MQTYNRTDLLLRLLNHYQAVPYLHKVIVVWNNVGEKGPDELWNSLGPHPVPVIFKLQTTNRMRNRLQVFP
          MQTYNRTDLLLRLLNHYQAVPYLHKVIV.WNNVGEKGPDELWNSLGPHPVPVIFKLQTTNR.RNRLQVFP
Retrocopy MQTYNRTDLLLRLLNHYQAVPYLHKVIVMWNNVGEKGPDELWNSLGPHPVPVIFKLQTTNRIRNRLQVFP

Parental  ELETNAVL-MVDDDTLISAQDLVFAFSVWQQFPDQIVGFVPRKHVSTSSGIYSYGGFELQTPGFGNGDQY
          ELETNAVL.MVDDDTLIS.QDLVFAFSVWQQFPDQIVGFVPRKHVSTSSGIYSYGGFELQTPGFGNGD.Y
Retrocopy ELETNAVL<MVDDDTLISTQDLVFAFSVWQQFPDQIVGFVPRKHVSTSSGIYSYGGFELQTPGFGNGDRY

Parental  SMVLIGASFFNSKYLDLFQRQPAAVHALIDEIQNCDDIAMNFIIAKHTGKTSGVFVKPVNMGNLEKESNG
          SMVLIGASFFNSKYLDLFQRQPAA.HALIDEIQNCDDIAMNFIIAKHTGKTSGVFV.PVNMGNLEKES.G
Retrocopy SMVLIGASFFNSKYLDLFQRQPAALHALIDEIQNCDDIAMNFIIAKHTGKTSGVFVEPVNMGNLEKESSG

Parental  GYPGMWHRAEHF
          GYPGMWHRAEHF
Retrocopy GYPGMWHRAEHF

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	0.04 RPM	50.61 RPM
SRP017611_brain	0.16 RPM	117.18 RPM
SRP017611_kidney	0.13 RPM	19.15 RPM
SRP017611_liver	0.07 RPM	10.95 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1594 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1594 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000020002	1 retrocopy	retro_cfam_1594 ,
Microcebus murinus	ENSMICG00000005233	1 retrocopy	retro_mmur_376,