RetrogeneDB ID: retro_cfam_2158

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:45815312..45816295(-)
• Located in intron of: ENSCAFG00000016427

Retrocopy information

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

Parental gene information

• Parental gene symbol: ST6GAL1
• Ensembl ID: ENSCAFG00000013698
• Aliases: None
• Description: None

Sequence

>retro_cfam_2158
CTCAGCAGTCCCCGGGGCCCAGCCAAGGCCAAGCCAGAGGCCTCCTTCCAGGTGTGGAACAAGTACAGCTCTTCCAAAAA
CCTTACCTCTAGGCTGCAGAAAATATGGAGGAATTATCTGAACGTGAAGGACTATAAAGTGTCTTATAAGGGGCTAGGGT
CTGACGGTCAAGTTCAGTGCAGAGGCCCTGCACTACCACCTCTGGGACCATGTGAATATATCCATAGTAGAGGCCACAGA
TTTTCCCTTCAACATTTCCGAATGGGTTTCCTGCCCAAGGAGAACGTTAGGACCAAGGCTGGGCCATGGGGCAGGTTTGC
TATTATCTCATCAGCAGGATCTCTGAAGTCCTCCCAGTTGGGCCAAGAAATAGATGATCACAGTGCAGTCCTGAGGTTTA
ATGAGGCATCCACAACCAGTTCCTCCCAAAATGTAGGCACAAAAACTACCATTCGCCTGATGACTCTCAGTTGGTCACCT
CTGCAGAGCACTTCCTCAAAGACAGTTTGTACAGTGAGGGATTCCTGATTGTTTGGGACCTGTCTGTTTGCATTCATATT
ATCTCAAAGTGGAAACAGAGCCCTGATTACAGCTTTTTTGAGAACTGTAAGAGCTGTTGCAAGCTACATCCTGATCAGCC
CTTTTATATCCTCAAGCCTGAAATGCCTTGAGAGCTGTGGGACATCATTCTTGAAGTCTCCCCAGAGGAAATTCAGCCAA
ATCCCCTATCCTCTGGGATGCTTAGCATCATCATTATCGTGATGCTGTGTGACCAAATGAATACTTACAAGTTTCTCCCA
TCCAAGGCAAGCCTTGGAGTGTGCTACTACTACCAGAAGTTCTTTGGCCGTACCTGTACAATGAGTACCTACCACCCACT
CCTCTTTGAGAAAAATTTGGTGAAGCACCTCAACCAGGGCACAGACAAGGACATTTATCTGCTTGGCAAAACTATACTGC
CTACCTTCCAGGGAATTCCCTGC

Alignment

ORF - retro_cfam_2158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.7 %
• Parental protein coverage: 82.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LGSPRGPVKAKSEASFQVWNKDSSSKNLIPRLQKIWRNYLNMNKYKVSYKGPGPG-VKFSAEALHCHLRD
          L.SPRGP.KAK.EASFQVWNK.SSSKNL..RLQKIWRNYLN...YKVSYKG.G...VKFSAEALH.HL.D
Retrocopy LSSPRGPAKAKPEASFQVWNKYSSSKNLTSRLQKIWRNYLNVKDYKVSYKGLGSD>VKFSAEALHYHLWD

Parental  HVNVSMVEATDFPFNTSEWEGFLPKENI-RTKAGPWGRCAVVSSAGSLKSSQLGREIDDHDAVLRFNGAP
          HVN.S.VEATDFPFN.SEW....P.....RTKAGPWGR.A..SSAGSLKSSQLG.EIDDH.AVLRFN.A.
Retrocopy HVNISIVEATDFPFNISEWVS-CPRRTL<RTKAGPWGRFAIISSAGSLKSSQLGQEIDDHSAVLRFNEAS

Parental  TASFQQDVGTKTTIRLM-NSQLVTTEGRFLKDSLYNEGILIVWDPSVYHSDIPKWYQSPDYSFFENYKSY
          T.S..Q.VGTKTTIRLM..SQLVT....FLKDSLY.EG.LIVWD.SV....I.KW.QSPDYSFFEN.KS.
Retrocopy TTSSSQNVGTKTTIRLM<DSQLVTSAEHFLKDSLYSEGFLIVWDLSVCIHIISKWKQSPDYSFFENCKSC

Parental  RKLHPDQPFYILKPQMPWELWDIIQEVSPEEIQPNPPSSGMLGIIIMMTLCDQVDIYEFLPSKRKTDVCY
          .KLHPDQPFYILKP.MP.ELWDII.EVSPEEIQPNP.SSGML.III...LCDQ...Y.FLPSK....VCY
Retrocopy CKLHPDQPFYILKPEMP*ELWDIILEVSPEEIQPNPLSSGMLSIIIIVMLCDQMNTYKFLPSKASLGVCY

Parental  YYQKFFDSACTMGAYHPLLFEKNLVKHLNQGTDEDIYLLGKATLPGFRRIRC
          YYQKFF...CTM..YHPLLFEKNLVKHLNQGTD.DIYLLGK..LP.F..I.C
Retrocopy YYQKFFGRTCTMSTYHPLLFEKNLVKHLNQGTDKDIYLLGKTILPTFQGIPC

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	44.27 RPM
SRP017611_brain	0.00 RPM	65.90 RPM
SRP017611_kidney	0.00 RPM	37.97 RPM
SRP017611_liver	0.00 RPM	441.46 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2158 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2158 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2158 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010357	1 retrocopy	retro_btau_1767,
Canis familiaris	ENSCAFG00000013698	1 retrocopy	retro_cfam_2158 ,
Felis catus	ENSFCAG00000013886	1 retrocopy	retro_fcat_1983,
Macaca mulatta	ENSMMUG00000014905	1 retrocopy	retro_mmul_630,
Nomascus leucogenys	ENSNLEG00000006676	1 retrocopy	retro_nleu_2774,
Pongo abelii	ENSPPYG00000014388	1 retrocopy	retro_pabe_3575,