RetrogeneDB ID: retro_cfam_2031

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: JH373331.1:58528..59604(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000007340
• Aliases: None
• Description: None

Sequence

>retro_cfam_2031
GTAGCGGCAGTGTCTGGCCTGATGCGGAGACCCCCGGAACAGGTGTCGGGATTGCTGAGGAGGCGCTTTCACCGGACGGC
GCTGGCGGCGCTGCAGGTGACAGTTCGTGAGGCTCTAAACCAAGGTACGGATGAAGAGCTGGAAAGAGATGAGAAGGTAT
TTATGCTTGGGGAAGAAGTTGCCCAGTATGATGGTGCATATAAGGTTAGTCGAGGCCTGTGGAAGAAATATGGCGATAAG
AGAATCATAGATACTCCCATATCTGAGATGGGCTTTGCTAGAATTGCCGTGGGTGCAGCTATGGCTGGGTTGAGGCCCAT
CTGTGAATTTATGACCTTCAATTTCTCTATGCAAGCCATTGACCAAGTTATAAATTCAGCTGCCAAGACCTACTACATGT
CGGGGGGCCTTCAGCCTGTGCCTATAGTCTTCAGGGGCCCAATGGTGCCTCAGCAGGCGTGGCTGCCCAACACTCCCAGT
GCTTTGCTGCCTGGTATGGGCACTGCCCAGGCTTAAAGGTGGTCAGCCCCTGGAATTCAGAGGATGCAAAAGGACTTATT
AAATCAGCCATTCGGGATAATAATCCAGTGGTGGTGCTAGAGAACGAACTGATGTATGGAGTTCCTTTTGAATTTCCCTC
CGAAGCTCAGTCAAAAGATTTTCTGATTCCCATTGGAAAAGCCAAAATAGAAAGGCAAGGTACACACATAACCGTAGTTG
CTCATTCAAGACCTGTGGGCCACTGCTTAGAAGCTGCAACAGTGTTATCCAAAGAGGGTATTGAATGTGAGGTGATAAAT
ATGTGAACCATCAGACCAATGGACATTGAAACAATAGAAGCCAGTGTCATGAAGACCAATCATCTCATAACTGTGGAAGG
AGGCTGGCCACAGTTTGGAGTAGGAGCTGAAATTTGTGCCAAGATTATGGAAGGCCCTGCATTCAATTTCCTGGATGCTC
CTGCAGTTCCTGTCACTGGTGCTGATGTCCCTATGCCTTATGCAAAGATTCTAGAAGACAACTCTGTACCTCAGGTTAAA
GACATCATATTTGCAATAAAGAAAACATTAAATATC

Alignment

ORF - retro_cfam_2031 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVSGLMRRPLEQVSGLLRRRFHRTAPAALQVTVREAINQGMDEELERDEKVFLLGEEVAQYDGAYKVS
          .AAVSGLMRRP.EQVSGLLRRRFHRTA.AALQVTVREA.NQG.DEELERDEKVF.LGEEVAQYDGAYKVS
Retrocopy VAAVSGLMRRPPEQVSGLLRRRFHRTALAALQVTVREALNQGTDEELERDEKVFMLGEEVAQYDGAYKVS

Parental  RGLWKKYGDKRIIDTPISEMGFAGIAVGAAMAGLRPICEFMTFNFSMQAIDQVINSAAKTYYMSGGLQPV
          RGLWKKYGDKRIIDTPISEMGFA.IAVGAAMAGLRPICEFMTFNFSMQAIDQVINSAAKTYYMSGGLQPV
Retrocopy RGLWKKYGDKRIIDTPISEMGFARIAVGAAMAGLRPICEFMTFNFSMQAIDQVINSAAKTYYMSGGLQPV

Parental  PIVFR-GPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNSEDAKGLIKSAIRDNNPVVVLENELMYGVP
          PIVFR.GPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNSEDAKGLIKSAIRDNNPVVVLENELMYGVP
Retrocopy PIVFR<GPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNSEDAKGLIKSAIRDNNPVVVLENELMYGVP

Parental  FEFPSEAQSKDFLIPIGKAKIERQGTHITVVAHSRPVGHCLEAATVLSKEGIECEVINMRTIRPMDIETI
          FEFPSEAQSKDFLIPIGKAKIERQGTHITVVAHSRPVGHCLEAATVLSKEGIECEVINM.TIRPMDIETI
Retrocopy FEFPSEAQSKDFLIPIGKAKIERQGTHITVVAHSRPVGHCLEAATVLSKEGIECEVINM*TIRPMDIETI

Parental  EASVMKTNHLITVEGGWPQFGVGAEICARIMEGPAFNFLDAPAVRVTGADVPMPYAKILEDNSVPQVKDI
          EASVMKTNHLITVEGGWPQFGVGAEICA.IMEGPAFNFLDAPAV.VTGADVPMPYAKILEDNSVPQVKDI
Retrocopy EASVMKTNHLITVEGGWPQFGVGAEICAKIMEGPAFNFLDAPAVPVTGADVPMPYAKILEDNSVPQVKDI

Parental  IFAIKKTLNI
          IFAIKKTLNI
Retrocopy IFAIKKTLNI

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	45.69 RPM
SRP017611_brain	0.08 RPM	34.06 RPM
SRP017611_kidney	0.13 RPM	113.45 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_2031 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2031 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2031 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021724	1 retrocopy	retro_btau_596,
Canis familiaris	ENSCAFG00000007340	2 retrocopies	retro_cfam_1215, retro_cfam_2031 ,
Callithrix jacchus	ENSCJAG00000019739	1 retrocopy	retro_cjac_3875,
Dasypus novemcinctus	ENSDNOG00000006937	1 retrocopy	retro_dnov_1090,
Monodelphis domestica	ENSMODG00000002398	1 retrocopy	retro_mdom_614,
Mus musculus	ENSMUSG00000021748	1 retrocopy	retro_mmus_290,
Oryctolagus cuniculus	ENSOCUG00000015632	1 retrocopy	retro_ocun_342,
Procavia capensis	ENSPCAG00000016595	1 retrocopy	retro_pcap_261,
Sarcophilus harrisii	ENSSHAG00000008480	1 retrocopy	retro_shar_5,
Ictidomys tridecemlineatus	ENSSTOG00000019553	2 retrocopies	retro_itri_1349, retro_itri_249,
Tupaia belangeri	ENSTBEG00000016148	2 retrocopies	retro_tbel_1651, retro_tbel_3170,