RetrogeneDB ID: retro_cfam_574

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:41584661..41585404(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000004696
• Aliases: None
• Description: None

Sequence

>retro_cfam_574
GAAAATGCTGTTGACTTAGAGGGCCCACCTTCAGACTTCTACTATATTAATGAATACAAACCAGCTCCTGGAATCAGCTT
AGTCAATGAAGCTGCCTTTGGTTGTTCATGTACAGATTGCTTCTTTGAGAAATGTTGTCCAGCTGAAGCTGGAGTTCTTT
TGGCTCATAATAAAAACCGGCAAATTAAAATCCCACCTGGTACCCCCATTTATGAATGCAACTCGAGGTGTCAATGCGGA
CCCGATTGTCCCAATAGGATTGTACTCAAAGGCACCCAGTATTCACTTTGCATCTTCTGAACTAGCAATGGCTGTGGCTG
GGGTGTAAAAACCCTTGTGAAGATTAAAAGAATGAGTTTTGTCATGGAATACGCTGGAGAGGTAATCACAAGCGAAGAAT
CTGAAAGACAGGGGCAGTTATATTCCCCAACAAGGGAATCACATATCTCTTTGATCTGGATTATGAATCTGATGAATTCA
CAGTGGATGCAGCCCGATATGGAAATGGCTCTCATTTTGTTAATCACAGTTTTGACCTAAATCTTCAGGTGTTCAATGTT
TTCATTGACAACCTTGATACCCATCTTCCGCGAATAGCATTATTTTCCACGAGAACTATAAATGCTGGATAAGAGCTCAT
TTTTGATGATCAGATGAAAGGTTCTTCAGATTCCGTTGACCACAGCCCAGCCAAAAAGAGGGTCAGGACCGTGTGCAAGT
GTGGAGCTGTGGCTTGCAGAGGT

Alignment

ORF - retro_cfam_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.33 %
• Parental protein coverage: 61.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ENTVDLEGPPSDFYYINEYKPAPGISLVNEATFGCSCTDCFFEKCCPAEAGVLLAYNKNQQIKIPPGTPI
          EN.VDLEGPPSDFYYINEYKPAPGISLVNEA.FGCSCTDCFFEKCCPAEAGVLLA.NKN.QIKIPPGTPI
Retrocopy ENAVDLEGPPSDFYYINEYKPAPGISLVNEAAFGCSCTDCFFEKCCPAEAGVLLAHNKNRQIKIPPGTPI

Parental  YECNSRCQCGPDCPNRIVQKGTQYSLCIFRTSNGCGWGVKTLVKIKRMSFVMEYVGEVITSEEAER-RGQ
          YECNSRCQCGPDCPNRIV.KGTQYSLCIF.TSNGCGWGVKTLVKIKRMSFVMEY.GEVITSEE.ER.RG.
Retrocopy YECNSRCQCGPDCPNRIVLKGTQYSLCIF*TSNGCGWGVKTLVKIKRMSFVMEYAGEVITSEESER>RGS

Parental  -LYDNKGITYLFDLDYESDEFTVDAARYGNVSHFVNHSCDPNLQVFNVFIDNLDTRLPRIALFSTRTINA
          ....NKGITYLFDLDYESDEFTVDAARYGN.SHFVNHS.D.NLQVFNVFIDNLDT.LPRIALFSTRTINA
Retrocopy >IFPNKGITYLFDLDYESDEFTVDAARYGNGSHFVNHSFDLNLQVFNVFIDNLDTHLPRIALFSTRTINA

Parental  GEELTFDYQMKGSGDISSDSVDHSPAKKRVRTVCKCGAVTCRG
          G.EL.FD.QMKGS.D....SVDHSPAKKRVRTVCKCGAV.CRG
Retrocopy G*ELIFDDQMKGSSD----SVDHSPAKKRVRTVCKCGAVACRG

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	6.34 RPM
SRP017611_brain	0.00 RPM	6.19 RPM
SRP017611_kidney	0.00 RPM	9.11 RPM
SRP017611_liver	0.00 RPM	2.39 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_574 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_574 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	ENSCAFG00000004696	1 retrocopy	retro_cfam_574 ,
Cavia porcellus	ENSCPOG00000008492	1 retrocopy	retro_cpor_1546,
Homo sapiens	ENSG00000152455	1 retrocopy	retro_hsap_3482,
Gorilla gorilla	ENSGGOG00000028243	1 retrocopy	retro_ggor_2348,
Microcebus murinus	ENSMICG00000002803	1 retrocopy	retro_mmur_340,
Nomascus leucogenys	ENSNLEG00000012108	1 retrocopy	retro_nleu_2202,
Oryctolagus cuniculus	ENSOCUG00000015090	1 retrocopy	retro_ocun_1408,
Ochotona princeps	ENSOPRG00000009465	1 retrocopy	retro_opri_1005,
Pongo abelii	ENSPPYG00000002106	1 retrocopy	retro_pabe_2877,
Tupaia belangeri	ENSTBEG00000006477	4 retrocopies	retro_tbel_2646, retro_tbel_3572, retro_tbel_852, retro_tbel_993,