RetrogeneDB ID: retro_cfam_1612

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 37:19967558..19968478(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABCF2
• Ensembl ID: ENSCAFG00000004830
• Aliases: None
• Description: ATP-binding cassette, sub-family F (GCN20), member 2 [Source:HGNC Symbol;Acc:71]

Sequence

>retro_cfam_1612
CCCTCTGACCTGGCCAAGAAGAAGGCAGCCAAAAAGAAGGAAGCTGCCAAAGCACAACAGCGGCCCAGAAAGGGACACGA
GGAAAATGGAGATACTGTCACAGAACCACAGGTGGCAAAGGAGAAAAATGAGGAGGCCAATGGCCGAGAGACCACAGAAG
TGGATTTTCTGACCAAGGAGCTAGAGGACTTTGAGATGAAGAAAGCTGCTGCTTGAGCTGTCACTGGTGTCCTTGCCTCT
CACCCCAACAGCACTGCAGCCCACATTATCAACCTCTCCCTCACCTTTCATGGTCAAGAGCTAATCAGTGACACCAAAAG
GAATTAAACTCGGGCCATCATTATGGCCTCATTGGCTTACACGGAATTAGAGAGTCCATGCTGCTCTCTGCTACTGGGAA
ACGGGAAGTGCCCACCCCTGAGCACATTGACATCTACCATCTGACTCAGGAGATGCCCTCTAGTGACAAGACACCCTTGT
AGTGTGTGATGGAAGTCGACACAGAGCAGGCCATGCCGGAGAGGGAGGCTGAGCAGCTGGCTCACGAGGATGCTGAGTGT
GAGAAGCTCATGGAGCTCTACAAGTGACTGGCGGAGCTGGATGTTGACAAGGTGGAAATGAGGGCTTCCCAGAACCTGCA
TGGACTGGGTTTCATTCCTGCCATGCAGCGCAAGAAGCTGAAAGACTTCAGTGGGGGCTGGAAAATGAGGGTTGCCCTCG
CCAGAGCCCTCTTCACTCAGCCCTTCATGCTGCTCCTGGACAAGCCCACCAACCACCTGGATCTCGAGGCTTCTGTGTGG
TTGGAAGAAGAATTAAAGACTTATAAGCACATCCTGGTCCTCGTCTCCCATTCCCAGGACCTTCTGAATGGTGTCTATAC
CAACATCATTCATATGCACAACAAGAAACTGAAGTATTAC

Alignment

ORF - retro_cfam_1612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 93.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSDLAKKKAAKKKEAAKARQRPRKGHEENGDTVTEPQVAEEKSE-ANGRETTELDLLTKELEDFEMKKAA
          PSDL.............A.QRPRKGHEENGDTVTEPQVA.EK.E.ANGRETTE.D.LTKELEDFEMKKAA
Retrocopy PSDLXXXXXXXXXXXXXAQQRPRKGHEENGDTVTEPQVAKEKNEEANGRETTEVDFLTKELEDFEMKKAA

Parental  ARAVTGVLASHPNSTDAHIINLSLTFHGQELLSDTKL-ELNSGRRYGLIGLNGIGKSMLLSAIGKREVPI
          A.AVTGVLASHPNST.AHIINLSLTFHGQEL.SDTK..ELNSG..YGLIGL.GI..SMLLSA.GKREVP.
Retrocopy A*AVTGVLASHPNSTAAHIINLSLTFHGQELISDTKR<ELNSGHHYGLIGLHGIRESMLLSATGKREVPT

Parental  PEHIDIYHLTREMPPSEKTPLQCVMEVDTERAMLEREAERLAHEDAECEKLMELYERLEELDADKAEMRA
          PEHIDIYHLT.EMP.S.KTPL.CVMEVDTE.AM.EREAE.LAHEDAECEKLMELY..L.ELD.DK.EMRA
Retrocopy PEHIDIYHLTQEMPSSDKTPL*CVMEVDTEQAMPEREAEQLAHEDAECEKLMELYK*LAELDVDKVEMRA

Parental  SRILHGLGFTPAMQRKKLKDFSGGWRMRVALARALFIRPFMLLLDEPTNHLDLDACVWLEEELKTFKRIL
          S..LHGLGF.PAMQRKKLKDFSGGW.MRVALARALF..PFMLLLD.PTNHLDL.A.VWLEEELKT.K.IL
Retrocopy SQNLHGLGFIPAMQRKKLKDFSGGWKMRVALARALFTQPFMLLLDKPTNHLDLEASVWLEEELKTYKHIL

Parental  VLVSHSQDFLNGVCTNIIHMHNKKLKYY
          VLVSHSQD.LNGV.TNIIHMHNKKLKYY
Retrocopy VLVSHSQDLLNGVYTNIIHMHNKKLKYY

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	0.08 RPM	17.72 RPM
SRP017611_brain	0.08 RPM	21.99 RPM
SRP017611_kidney	0.00 RPM	9.71 RPM
SRP017611_liver	0.07 RPM	6.24 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1612 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1612 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004830	1 retrocopy	retro_cfam_1612 ,
Callithrix jacchus	ENSCJAG00000020371	3 retrocopies	retro_cjac_1859, retro_cjac_3526, retro_cjac_381,
Dipodomys ordii	ENSDORG00000012672	1 retrocopy	retro_dord_334,
Echinops telfairi	ENSETEG00000008032	2 retrocopies	retro_etel_1041, retro_etel_1058,
Macaca mulatta	ENSMMUG00000006679	1 retrocopy	retro_mmul_1414,
Oryctolagus cuniculus	ENSOCUG00000000245	1 retrocopy	retro_ocun_765,