RetrogeneDB ID: retro_cfam_2107

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:84801147..84801636(+)
• Located in intron of: ENSCAFG00000018196

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM4
• Ensembl ID: ENSCAFG00000015796
• Aliases: None
• Description: tropomyosin 4 [Source:HGNC Symbol;Acc:12013]

Sequence

>retro_cfam_2107
GAGCAAGAGAGGAATGAAGGTGATAGAAAACTGGGCCATGAAAAAAAAAAAAAACGGGCCATGAAAGATGAGAAGATGGA
GATTCAGGAAATGCAGCTCAAAGAGGCCAAGCACATCGCTGAGGAGGCCGACCGAAAGTAGGAGGCGGTGGCTTATAAAT
TGGTCATCCTGGAGGACTAGCTGGAGAGGGTGGAGGAGCATGCTGAGGTGTCTGAACTAAAATGTAGTAACCTAGAAGAA
GAACTCAAGAATGTCACTGACAATCTGAAGTCACTCGATGCTGCGTCTGAAGTTTCTGAAAAGGACGATAAATAAGAAGA
AATCAAACTTTTGTCTGACAAACTGAAAGAGGCCGAGACCTGTGCTGAATTTGCAGAGAGAATGGTTGCAAAACTGGAAA
AGACCATTGGTGACCTGGAAGAAAAGCTTGCCCAGGCCAAGGAAGAGAATATGGGCTTACATCAGACACTAAACGAACTT
AACTGTATA

Alignment

ORF - retro_cfam_2107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 59.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAEKAADESERGMKVIENRAMKDEEKMEIQEMQLKEAKHIAEEADRKYEEVARKLVILEGELERAEERAE
          E.E........G......RAMKD.EKMEIQEMQLKEAKHIAEEADRK.E.VA.KLVILE..LER.EE.AE
Retrocopy EQERNEGDRKLGHXXXXXRAMKD-EKMEIQEMQLKEAKHIAEEADRK*EAVAYKLVILED*LERVEEHAE

Parental  VSELKCGDLEEELKNVTNNLKSLEAASEKYSEKEDKYEEEIKLLSDKLKEAETRAEFAERTVAKLEKTID
          VSELKC..LEEELKNVT.NLKSL.AASE..SEK.DK..EEIKLLSDKLKEAET.AEFAER.VAKLEKTI.
Retrocopy VSELKCSNLEEELKNVTDNLKSLDAASE-VSEKDDK-*EEIKLLSDKLKEAETCAEFAERMVAKLEKTIG

Parental  DLEEKLAQAKEENVGLHQTLDQTLNELNCI
          DLEEKLAQAKEEN.GLHQTL....NELNCI
Retrocopy DLEEKLAQAKEENMGLHQTL----NELNCI

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	52.79 RPM
SRP017611_brain	0.00 RPM	36.52 RPM
SRP017611_kidney	0.00 RPM	37.38 RPM
SRP017611_liver	0.00 RPM	14.87 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2107 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2107 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2107 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004553	2 retrocopies	retro_btau_1604, retro_btau_1758,
Canis familiaris	ENSCAFG00000015796	1 retrocopy	retro_cfam_2107 ,
Canis familiaris	ENSCAFG00000016966	1 retrocopy	retro_cfam_2167,
Canis familiaris	ENSCAFG00000017311	4 retrocopies	retro_cfam_1278, retro_cfam_1678, retro_cfam_2089, retro_cfam_983,
Callithrix jacchus	ENSCJAG00000014135	1 retrocopy	retro_cjac_206,
Gorilla gorilla	ENSGGOG00000014510	4 retrocopies	retro_ggor_1836, retro_ggor_2665, retro_ggor_2801, retro_ggor_609,
Monodelphis domestica	ENSMODG00000014882	1 retrocopy	retro_mdom_1354,
Mus musculus	ENSMUSG00000031799	1 retrocopy	retro_mmus_1625,
Nomascus leucogenys	ENSNLEG00000005413	2 retrocopies	retro_nleu_1952, retro_nleu_469,
Pan troglodytes	ENSPTRG00000010637	10 retrocopies	retro_ptro_1002, retro_ptro_1109, retro_ptro_1341, retro_ptro_1342, retro_ptro_1750, retro_ptro_1768, retro_ptro_2648, retro_ptro_2694, retro_ptro_2830, retro_ptro_516,
Pteropus vampyrus	ENSPVAG00000009755	2 retrocopies	retro_pvam_186, retro_pvam_187,
Ictidomys tridecemlineatus	ENSSTOG00000024252	1 retrocopy	retro_itri_1858,
Tupaia belangeri	ENSTBEG00000012927	7 retrocopies	retro_tbel_1435, retro_tbel_2468, retro_tbel_3663, retro_tbel_3709, retro_tbel_3872, retro_tbel_4651, retro_tbel_482,
Tarsius syrichta	ENSTSYG00000010642	9 retrocopies	retro_tsyr_1377, retro_tsyr_1613, retro_tsyr_1642, retro_tsyr_1853, retro_tsyr_628, retro_tsyr_694, retro_tsyr_704, retro_tsyr_742, retro_tsyr_749,
Tursiops truncatus	ENSTTRG00000014542	2 retrocopies	retro_ttru_504, retro_ttru_839,