RetrogeneDB ID: retro_cfam_1416

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:11506053..11506532(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11A
• Ensembl ID: ENSCAFG00000012889
• Aliases: SEC11A, SEC11L1, SPC18
• Description: Canis lupus familiaris SEC11 homolog A (S. cerevisiae) (SEC11A), mRNA. [Source:RefSeq mRNA;Acc:NM_001003313]

Sequence

>retro_cfam_1416
CTGTATTATCAAGTCCTAAATTTTGGCATGATTGTCTCCTTGGCACTAATGATCTGGAAGAGGTTAATGCTCATAACTGG
AAGTCAAAGTCCAATTGTAGTGGTCCTCAGTGGCAGCACGGGACCTGCATTTCATAGAAGAGATCTCTTTTTAACAAATC
AAGTTGAAGATCCCACCCGATTGGGAGAAACTGGTGTTTTTAGGATAGAGGAAAGAGAGATTTCTATAGTTCGTGGAGTC
TTGAAGACTCACGCGAAGCAAAATGGATATATCAAATTTTTGACAAAAGGAGATAACACAGTTGATGACTGCGGCTATAT
AAACAAGCACAACACTGGCTAGAGAAGAAAGATGTCATGGGGAGAGTCAGGGAATTTGTGCCTTTTACTGGGATTGTGCT
GATCCTCACGAATGACTACCCTAAATTTAAGTGTGCAGTACTCTTTCGGCTGGGTTTATTTGTGCTAGTCCATCATGAG

Alignment

ORF - retro_cfam_1416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.53 %
• Parental protein coverage: 90.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LYYQVLNFGMIVSSALMIWKGLMVITGSESPIVVVLSGSMEPAFHRGDLLFLTNRVEDPIRVGEIVVFRI
          LYYQVLNFGMIVS.ALMIWK.LM.ITGS.SPIVVVLSGS..PAFHR.DL.FLTN.VEDP.R.GE..VFRI
Retrocopy LYYQVLNFGMIVSLALMIWKRLMLITGSQSPIVVVLSGSTGPAFHRRDL-FLTNQVEDPTRLGETGVFRI

Parental  EGREIPIVHRVLKIHEKQNGHIKFLTKGDNNAVDDRG-LYKQGQHWLEKKDVVGRARGFVPYIGIVTILM
          E.REI.IV..VLK.H.KQNG.IKFLTKGDN..VDD.G.LYKQ.QHWLEKKDV.GR.R.FVP..GIV.IL.
Retrocopy EEREISIVRGVLKTHAKQNGYIKFLTKGDNT-VDDCG<LYKQAQHWLEKKDVMGRVREFVPFTGIVLILT

Parental  NDYPKFKYAVLFLLGLFVLVHRE
          NDYPKFK.AVLF.LGLFVLVH.E
Retrocopy NDYPKFKCAVLFRLGLFVLVHHE

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	33.73 RPM
SRP017611_brain	0.00 RPM	14.29 RPM
SRP017611_kidney	0.00 RPM	70.07 RPM
SRP017611_liver	0.00 RPM	26.32 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1416 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1416 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1416 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012889	1 retrocopy	retro_cfam_1416 ,
Callithrix jacchus	ENSCJAG00000016146	1 retrocopy	retro_cjac_1496,
Felis catus	ENSFCAG00000029786	2 retrocopies	retro_fcat_1178, retro_fcat_1908,
Homo sapiens	ENSG00000140612	1 retrocopy	retro_hsap_4058,
Gorilla gorilla	ENSGGOG00000011129	1 retrocopy	retro_ggor_2726,
Monodelphis domestica	ENSMODG00000019364	1 retrocopy	retro_mdom_726,
Pongo abelii	ENSPPYG00000006881	1 retrocopy	retro_pabe_3333,
Pan troglodytes	ENSPTRG00000007404	1 retrocopy	retro_ptro_2751,
Tupaia belangeri	ENSTBEG00000012320	3 retrocopies	retro_tbel_1139, retro_tbel_2280, retro_tbel_745,
Tursiops truncatus	ENSTTRG00000005833	1 retrocopy	retro_ttru_1237,