RetrogeneDB ID: retro_cfam_1342

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:47022549..47022939(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM216
• Ensembl ID: ENSCAFG00000016171
• Aliases: None
• Description: transmembrane protein 216 [Source:HGNC Symbol;Acc:25018]

Sequence

>retro_cfam_1342
TCACCCCCACCACTCGAAATCCTGTTCTTTCTGAACAGGTGGTATTATGCTACCCCATTTCTTGCTGGAATTCTTCATAT
TTCTGTATAAAGCTCTCCTGCTACTATATCCAACGGCCAATATAGTACGAGGTGTGGTGATGCTTCTTTACCTTGGAATT
GAAGTATTTCGACTATCTTTTGATACAAAGGGAAATGGCTGCCAATTAAAGATGCCACTTGGTGTTAGCATGGCCTTGAC
CTTCCCATCGGCCATAATGGCCTCCTATTATCTGCTGCTGCAAACCAAGTGCTCTGCCTGGAAGCCATTCTGAACAGCAT
CTCGCTCTTCTGTGTTTCAGAGCTGCTGCTTGAGGTGCTCACCCTGACTACTCTTTCCAGTATGGACAGG

Alignment

ORF - retro_cfam_1342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.1 %
• Parental protein coverage: 93.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSTPLEILFFLNGWYYAT-YFLLELFIFLYKALLLPYPTANLVLDVVMLLLYLGIEVIRLFFGTKGNLCQ
          S..PLEILFFLN.WYYAT..FLLE.FIFLYKALLL.YPTAN.V..VVMLL.YLGIEV.RL.F.TKGN.CQ
Retrocopy SPPPLEILFFLNRWYYAT>HFLLEFFIFLYKALLLLYPTANIVRGVVMLL-YLGIEVFRLSFDTKGNGCQ

Parental  RKMPLGFSVALTFPSAMMASYYLLLQT-YVLRLEAIMNSILLFFCGSELLLEVLTLTAFSSMDR
          .KMPLG.S.ALTFPSA.MASYYLLLQT..VL.LEAI.NSI.L.FC.SELLLEVLTLT..SSMDR
Retrocopy LKMPLGVSMALTFPSAIMASYYLLLQT<QVLCLEAILNSISL-FCVSELLLEVLTLTTLSSMDR

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	2.69 RPM
SRP017611_brain	0.00 RPM	2.62 RPM
SRP017611_kidney	0.00 RPM	7.79 RPM
SRP017611_liver	0.00 RPM	2.18 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1342 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1342 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016592	1 retrocopy	retro_amel_1255,
Bos taurus	ENSBTAG00000021517	1 retrocopy	retro_btau_1184,
Canis familiaris	ENSCAFG00000016171	4 retrocopies	retro_cfam_1342 , retro_cfam_331, retro_cfam_332, retro_cfam_333,
Monodelphis domestica	ENSMODG00000020362	1 retrocopy	retro_mdom_232,
Mustela putorius furo	ENSMPUG00000014169	4 retrocopies	retro_mputfur_1341, retro_mputfur_1536, retro_mputfur_1537, retro_mputfur_1538,
Oryctolagus cuniculus	ENSOCUG00000001682	1 retrocopy	retro_ocun_799,