RetrogeneDB ID: retro_cfam_1860

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:69210944..69212003(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB
• Ensembl ID: ENSCAFG00000000443
• Aliases: None
• Description: None

Sequence

>retro_cfam_1860
ATAAGGGAAATTGTGCACATCCAGGCCGGTCAATGTGGTGACCAGACAGGTGCCAAGTTCTGGGAGGTCATCAGTGATGA
ACACGGCATCGATCCCACCAGAACCTACCACGGTGACAACGACCTGCAGCTGGATCATATCTCCATGTACTACAATGAAG
CTACAGGTGGCAAATACGTACCTTGCCCTATGTTGGTGGATCTAGAACCCGGGACCATGGACTCTGTTCGCTCAGGTCCT
TTAGGGCAGATATTCAGACCAGAAAACTTTGTTTTTGGGCAGTCTGGGGCTGGCAACAACTGGGCCAAGGGCCACTACAC
AGAGGGGGCTGAGCTAGTGGACTCAATCCTGGATGTGGTGCAGAAGGAAGCTGAGAGCTGTGACTGCCTGCAGGGCTTCC
AGCTGACCCACTCACTGGGCAGGGGCACGGGTTCTGGCATGGGCACGCTGCTCATCAGCAAGATCCGAGAAGAGTACCTT
GACCGCATCATGAACACCTTCAGTGTGGTGCCCTCCCCCAAAGTGTCTGACACAGTGGTTGAGCCCTACAATGTCACCCT
CTCCATCCATCAGTTGGTAGAGAACACAGATGAGATCTATTGCATTGAAAATGAGGCCCTGTATGACATCTGCTTCCGCA
CCCTCAAGCTGACCACGCCAACCTATGGGGACCTCAACCACCTTGTCTCAGCCACCATGAGTGGTGTCACCACCTGCTTC
CGCATCCCTGGTCAGCTCAATGCTGACCTCCGCAAGCTGGCAGTCAACATGGTGCCCTTCCCACGTCTCCACTTCTTCAT
GCCTGGCTTTGCACCTCTGACCAGCCGTGGAAGCCAGCAGTATCAGGCCCTCACTGTGCCTGAACTCACCAGGCAAGGCT
TTGATGCCAAGAACATGATGGCTGCCTGTGACCCCCGCCATGGCCATTACCTCACTGTGGCTGCTGTCTTCCGTGGGTGG
ATGTCCATGAAGGAGGTAGATGAGCAGATGCTCAATGTGCAAAACAAGAATAGTAGTTACTTCGTGGAATGGATCCCCAA
CAATGCCAAGTCCGCTGTG

Alignment

ORF - retro_cfam_1860 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.78 %
• Parental protein coverage: 79.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEP
          .REIVHIQAGQCG.Q.GAKFWEVISDEHGIDPT.TYHGD.DLQLD.IS.YYNEATGGKYVP...LVDLEP
Retrocopy IREIVHIQAGQCGDQTGAKFWEVISDEHGIDPTRTYHGDNDLQLDHISMYYNEATGGKYVPCPMLVDLEP

Parental  GTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
          GTMDSVRSGP.GQIFRP.NFVFGQSGAGNNWAKGHYTEGAELVDS.LDVV.KEAESCDCLQGFQLTHSLG
Retrocopy GTMDSVRSGPLGQIFRPENFVFGQSGAGNNWAKGHYTEGAELVDSILDVVQKEAESCDCLQGFQLTHSLG

Parental  GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
          .GTGSGMGTLLISKIREEY.DRIMNTFSVVPSPKVSDTVVEPYN.TLS.HQLVENTDE.YCI.NEALYDI
Retrocopy RGTGSGMGTLLISKIREEYLDRIMNTFSVVPSPKVSDTVVEPYNVTLSIHQLVENTDEIYCIENEALYDI

Parental  CFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQ
          CFRTLKLTTPTYGDLNHLVSATMSGVTTC.R.PGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQ
Retrocopy CFRTLKLTTPTYGDLNHLVSATMSGVTTCFRIPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQ

Parental  YRALTVPELTQQVFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVK
          Y.ALTVPELT.Q.FDAKNMMAACDPRHG.YLTVAAVFRG.MSMKEVDEQMLNVQNKNSSYFVEWIPNN.K
Retrocopy YQALTVPELTRQGFDAKNMMAACDPRHGHYLTVAAVFRGWMSMKEVDEQMLNVQNKNSSYFVEWIPNNAK

Parental  TAV
          .AV
Retrocopy SAV

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	453.80 RPM
SRP017611_brain	0.24 RPM	227.30 RPM
SRP017611_kidney	0.07 RPM	40.68 RPM
SRP017611_liver	0.00 RPM	35.75 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1860 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1860 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1860 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006969	2 retrocopies	retro_btau_471, retro_btau_55,
Canis familiaris	ENSCAFG00000000443	1 retrocopy	retro_cfam_1860 ,
Echinops telfairi	ENSETEG00000013572	1 retrocopy	retro_etel_641,
Macaca mulatta	ENSMMUG00000023684	2 retrocopies	retro_mmul_2501, retro_mmul_375,
Mustela putorius furo	ENSMPUG00000011690	3 retrocopies	retro_mputfur_1123, retro_mputfur_607, retro_mputfur_807,
Nomascus leucogenys	ENSNLEG00000005348	1 retrocopy	retro_nleu_498,
Otolemur garnettii	ENSOGAG00000032213	1 retrocopy	retro_ogar_2391,
Pongo abelii	ENSPPYG00000016419	4 retrocopies	retro_pabe_2920, retro_pabe_3210, retro_pabe_3698, retro_pabe_467,