RetrogeneDB ID: retro_cfam_1215

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:6536334..6537401(+)
• 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_1215
CTGATGCAGAGACCCCTTGAAAAGGTGTCTGGGCTGCTGAGGAGGCACTTCCACTGGATAGCGCCTGTGGTGCTGCAGGT
GACAGTCTGTGAGGCTATAAACCAAAGTATGGATGAGGAGCTGGAAAGAGATGAGAAGGTATTTCTACTTGGGGAAGAAG
TTGCCCAGTATGATGGCACATATAAGGTTAGTCAAGGCCTGTGGAAGATATATGGCAATAAGAGAATCATAGATATTCCC
ATATATGAGAGGGGCTTTGCTGGAAATGCCGTGGGTACAGCTATGGGTGGGTTGAGGCCCATCTGTGAATTTATGACCTT
CAATTTCTCTATGTAAGCTATTGACCAGGTTATAAATTCAGCTGCCAAGACCTACTTACTACATGTTGGAGGGCCTTCCG
CCTATGCCTATAGTCTTCAGGGGGCCCAATGACACCTCAGCAGGCATGGCTGCCCAACACTCACAGTGCTTTGCTGCCCA
GTATGGGCACTGCCCAGGCTTAAAGGTGGTCAGCCCCTGGAATTCAGAGGATGCAAAAGGACTTATTAAATCAGCCATTC
GGGATAATAATCCAGTGGTGGTGCTAGAGGACGAACTGATGTATGGAGTTCCTTTTGAATTTCCCTCCGAAGCTCAGTCA
AAAGATCTTCTGATTCCCATTGGAAAAGCCAAAATAGAAAGGCAAGGGACACACATAACCATAGTTGCCCATTCAAAACC
TGTGGGCCACTGCTTAGAAGCTGCAACAGTGCTATCCAAAGAGGGTATTGAATGTGAGGTGATAAATACGCGAACTATCA
GACCGATGGACATTGAAACAAAAGAAGCCTGTGTCATGAAGACCAATCATCTCATAACTGTGGGAAGGAGGCTGGCCACA
GTTTGGAGTAAGAGCTGAAATTTGTGGCAGGATCATGGAAGGCCCTGCATTCAATTTCCTGGATGCTCCTGCAGTTCGTG
TCACTGGTGCTGATGTCCCTATGCCTTATGCAAAGATTCTAGAAGACAACTCTGTACCTCAGGTTAAAGACATCAAATTT
GCAATTTAAAAAAACACATTAAATATC

Alignment

ORF - retro_cfam_1215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.68 %
• Parental protein coverage: 98.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LMRRPLEQVSGLLRRRFHRTAPAALQVTVREAINQGMDEELERDEKVFLLGEEVAQYDGAYKVSRGLWKK
          LM.RPLE.VSGLLRR.FH..AP..LQVTV.EAINQ.MDEELERDEKVFLLGEEVAQYDG.YKVS.GLWK.
Retrocopy LMQRPLEKVSGLLRRHFHWIAPVVLQVTVCEAINQSMDEELERDEKVFLLGEEVAQYDGTYKVSQGLWKI

Parental  YGDKRIIDTPISEMGFAGIAVGAAMAGLRPICEFMTFNFSMQAIDQVINSAAKTYYMS-GG-LQPVPIVF
          YG.KRIID.PI.E.GFAG.AVG.AM.GLRPICEFMTFNFSM.AIDQVINSAAKTY....GG.L.P.PIVF
Retrocopy YGNKRIIDIPIYERGFAGNAVGTAMGGLRPICEFMTFNFSM*AIDQVINSAAKTYLLHVGG>LPPMPIVF

Parental  RGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWNSEDAKGLIKSAIRDNNPVVVLENELMYGVPFEFPS
          RGPN..SAG.AAQHSQCFAA.YGHCPGLKVVSPWNSEDAKGLIKSAIRDNNPVVVLE.ELMYGVPFEFPS
Retrocopy RGPNDTSAGMAAQHSQCFAAQYGHCPGLKVVSPWNSEDAKGLIKSAIRDNNPVVVLEDELMYGVPFEFPS

Parental  EAQSKDFLIPIGKAKIERQGTHITVVAHSRPVGHCLEAATVLSKEGIECEVINMRTIRPMDIETIEASVM
          EAQSKD.LIPIGKAKIERQGTHIT.VAHS.PVGHCLEAATVLSKEGIECEVIN.RTIRPMDIET.EA.VM
Retrocopy EAQSKDLLIPIGKAKIERQGTHITIVAHSKPVGHCLEAATVLSKEGIECEVINTRTIRPMDIETKEACVM

Parental  KTNHLITV-EGGWPQFGVGAEICARIMEGPAFNFLDAPAVRVTGADVPMPYAKILEDNSVPQVKDIIFAI
          KTNHLITV.EGGWPQFGV.AEIC.RIMEGPAFNFLDAPAVRVTGADVPMPYAKILEDNSVPQVKDI.FAI
Retrocopy KTNHLITV>EGGWPQFGVRAEICGRIMEGPAFNFLDAPAVRVTGADVPMPYAKILEDNSVPQVKDIKFAI

Parental  -KKTLNI
          .K.TLNI
Retrocopy *KNTLNI

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	45.69 RPM
SRP017611_brain	0.00 RPM	34.06 RPM
SRP017611_kidney	0.07 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_1215 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1215 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1215 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,