RetrogeneDB ID: retro_cfam_1356

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:74185322..74186097(+)
• Located in intron of: ENSCAFG00000016208

Retrocopy information

• Ensembl ID: ENSCAFG00000023576
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BCCIP
• Ensembl ID: ENSCAFG00000012873
• Aliases: None
• Description: BRCA2 and CDKN1A interacting protein [Source:HGNC Symbol;Acc:978]

Sequence

>retro_cfam_1356
GAAGTGAATGTTGAATTTGAAGCTTATTCCATCTCCGACAAGGATCATGACGGAATTAAGAAATTATTGCAACAGCTTTT
CCTAAAGGCTCCTGTGAACACTGCAGAACTAAGTGATCTCTCAATTCAACAAAACCATATTGGGAGTGTGATAAAGCAGA
CGGATGTTTCAGAAGACAGCGATGACGATGTGGATGAAGATGAGATTTTTGGGTTCATAAGTCTTTTAAATTTAACTGAA
AGAAAGGGAACCCGGTGTGCTGAACAAATTAAAGAGGTGATCCTGAGCTCCTGTGAGAAGAACTGTGGAAAGAGTTTGGT
GGAACAGCTGGATACACTTTTAAACGACAACTCCAAGCCTGTGGGCTTTCTCCTCAGCGAGAGGTTCGTTAACGTCCCTC
CTCAGATTGCGCTGCCCATGCACCAGCAGCTCCAGAAAGAACTAGCAGAGGCACACAAAACTAACAAGCCGTGTGGGAAG
TGTTACTTCTACCTTCTGATTAGCAAGACGTTTGTGGAAGCTGGAAAAAATTCCAAAAAGAAAGGGAGCAACCAAGAAGA
GAAAGAGGAGTAATGTTTGCAAATGCAGAGGAAGAATTTTTCTATGAGAAGGCCATCCTGAAGTTCAGCTACTCGGTGCA
GGAAGAGAGCGACACTCGTCTGGGAGGCAGGTGGTCCTGTGAGGACACCCCATGAAGCCCTTGTGAACCGTGATGTTGAT
TCCAGGTGACCGGATGAACGAAATCATGGACAGACTGAAAGAGCACCTCTCCATG

Alignment

ORF - retro_cfam_1356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.25 %
• Parental protein coverage: 82.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EVNVEFEAYSISDKDHDGIKKLLQQLFLKAPVNTAELTDLLIQQNHIGSVIKQTDVSEDSDDDVDEDEIF
          EVNVEFEAYSISDKDHDGIKKLLQQLFLKAPVNTAEL.DL.IQQNHIGSVIKQTDVSEDSDDDVDEDEIF
Retrocopy EVNVEFEAYSISDKDHDGIKKLLQQLFLKAPVNTAELSDLSIQQNHIGSVIKQTDVSEDSDDDVDEDEIF

Parental  GFISLLNLTERKGTQCVEQIKELILSSCEKNCGKSLVEQLDTLLNDNSKPVGFLLSERFINVPPQIALPM
          GFISLLNLTERKGT.C.EQIKE.ILSSCEKNCGKSLVEQLDTLLNDNSKPVGFLLSERF.NVPPQIALPM
Retrocopy GFISLLNLTERKGTRCAEQIKEVILSSCEKNCGKSLVEQLDTLLNDNSKPVGFLLSERFVNVPPQIALPM

Parental  HQQLQKELAEAHKTNKPCGKCYFYLLISKTFVEAGKNSKKKGSNQEEKEE-LMFANAEEEFFYEKAILKF
          HQQLQKELAEAHKTNKPCGKCYFYLLISKTFVEAGKNSKKKGSNQEEKEE..MFANAEEEFFYEKAILKF
Retrocopy HQQLQKELAEAHKTNKPCGKCYFYLLISKTFVEAGKNSKKKGSNQEEKEE<VMFANAEEEFFYEKAILKF

Parental  SYSVQEESDTRLGGRWSFDDV-PMKPLRTVMLIPGDRMDEIMDRLKEHLSV
          SYSVQEESDTRLGGRWS..D..PMKPL.TVMLIPGDRM.EIMDRLKEHLS.
Retrocopy SYSVQEESDTRLGGRWSCEDT<PMKPL*TVMLIPGDRMNEIMDRLKEHLSM

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	37.50 RPM
SRP017611_brain	0.08 RPM	16.04 RPM
SRP017611_kidney	0.13 RPM	44.24 RPM
SRP017611_liver	0.00 RPM	15.59 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1356 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1356 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1356 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012873	1 retrocopy	retro_cfam_1356 ,
Callithrix jacchus	ENSCJAG00000012411	1 retrocopy	retro_cjac_2838,
Dasypus novemcinctus	ENSDNOG00000002939	1 retrocopy	retro_dnov_530,
Macaca mulatta	ENSMMUG00000008541	1 retrocopy	retro_mmul_472,
Oryctolagus cuniculus	ENSOCUG00000008761	1 retrocopy	retro_ocun_843,
Otolemur garnettii	ENSOGAG00000010901	1 retrocopy	retro_ogar_1184,
Ictidomys tridecemlineatus	ENSSTOG00000011828	4 retrocopies	retro_itri_1004, retro_itri_1130, retro_itri_1513, retro_itri_559,
Tupaia belangeri	ENSTBEG00000002570	4 retrocopies	retro_tbel_1259, retro_tbel_1260, retro_tbel_2963, retro_tbel_3044,