RetrogeneDB ID: retro_cjac_393

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:46061598..46062198(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021951
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ITGB1BP1
• Ensembl ID: ENSCJAG00000006250
• Aliases: None
• Description: integrin beta 1 binding protein 1 [Source:HGNC Symbol;Acc:23927]

Sequence

>retro_cjac_393
ATGTTTCGCAAAGGCAAAAAACGACACAGTAGTAGCCGTTCCCAATGTAGTGAAATCAGTACTAAGAGCAAGTCTGTAGA
TTCTAGCCTTGGGGGTCTTTCACGATCCAGCACTGTGGCCAGCCTCGACACAGATTCCACCAGAAGCTCAGGACAAAGCA
ACAGTAATTCAGATAGCTGTGCAGAATTTCGAATAAAATATGTTGATGCCATTGAGAAACTGAAACTCTCTGAGGGAAAA
GGTCTTGAAGGACCCTTGGACCTGATAAACTATATAGATGTTGCTCAGCAAGATGGAAAGTTGTCTTTTGTTCCTCCGGA
GGAAGAATTTATTATGGGAATTTCCAAGTATGACATAAAAGTATCAACATCAGATCAATATGATGTTTTGCACAGGCATG
CTCTCTTCTTAATAATCCGGATGGTGTGTTACGATGATGGTCTGGTGACAGGAAAAAGCTTACTGGATCTGAAGACCACA
GATGCAAGCAATGAAGAATACAGCCTGTGGGTGTATCAGTGCAACAGCCTGGAACAAGCACAAGCCGTTTGCAAGGTTTT
ATCCACCGCTTTTGACTCTGTATTCACATCTGAGAAACCT

Alignment

ORF - retro_cjac_393 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFRKGKKRHSSSSSQSSEISTKSKSVDSSLGGLSRSSTVASLDTDSTKSSGQSNSNSDTCAEFRIKYVGA
          MFRKGKKRHSSS.SQ.SEISTKSKSVDSSLGGLSRSSTVASLDTDST.SSGQSNSNSD.CAEFRIKYV.A
Retrocopy MFRKGKKRHSSSRSQCSEISTKSKSVDSSLGGLSRSSTVASLDTDSTRSSGQSNSNSDSCAEFRIKYVDA

Parental  IEKLKLSEGEGLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLIIR
          IEKLKLSEG.GLEGPLDLINYIDVAQQDGKL.FVPPEEEFIMG.SKY.IKVSTSDQYDVLHRHAL.LIIR
Retrocopy IEKLKLSEGKGLEGPLDLINYIDVAQQDGKLSFVPPEEEFIMGISKYDIKVSTSDQYDVLHRHALFLIIR

Parental  MVCYDDGLGAGKSLLALKTTDASNEEYSLWVYQCNSLEQAQAICKVLSTAFDSVLTSEKP
          MVCYDDGL..GKSLL.LKTTDASNEEYSLWVYQCNSLEQAQA.CKVLSTAFDSV.TSEKP
Retrocopy MVCYDDGLVTGKSLLDLKTTDASNEEYSLWVYQCNSLEQAQAVCKVLSTAFDSVFTSEKP

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
SRP051959_colon	0.00 RPM	6.41 RPM
SRP051959_heart	0.02 RPM	11.19 RPM
SRP051959_kidney	0.02 RPM	6.39 RPM
SRP051959_liver	0.00 RPM	5.59 RPM
SRP051959_lung	0.03 RPM	9.16 RPM
SRP051959_lymph_node	0.02 RPM	9.93 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.67 RPM
SRP051959_spleen	0.00 RPM	8.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_393 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_393 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_393 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013063	2 retrocopies	retro_btau_1221, retro_btau_1435,
Choloepus hoffmanni	ENSCHOG00000013602	2 retrocopies	retro_chof_1385, retro_chof_432,
Callithrix jacchus	ENSCJAG00000006250	3 retrocopies	retro_cjac_1650, retro_cjac_2776, retro_cjac_393 ,
Dasypus novemcinctus	ENSDNOG00000008930	3 retrocopies	retro_dnov_1422, retro_dnov_2198, retro_dnov_727,
Homo sapiens	ENSG00000119185	1 retrocopy	retro_hsap_277,
Gorilla gorilla	ENSGGOG00000001754	1 retrocopy	retro_ggor_321,
Macropus eugenii	ENSMEUG00000006761	1 retrocopy	retro_meug_1434,
Microcebus murinus	ENSMICG00000002359	7 retrocopies	retro_mmur_1251, retro_mmur_1342, retro_mmur_1375, retro_mmur_1523, retro_mmur_1539, retro_mmur_244, retro_mmur_442,
Myotis lucifugus	ENSMLUG00000010629	2 retrocopies	retro_mluc_1218, retro_mluc_1752,
Macaca mulatta	ENSMMUG00000018036	1 retrocopy	retro_mmul_563,
Nomascus leucogenys	ENSNLEG00000013322	1 retrocopy	retro_nleu_1488,
Oryctolagus cuniculus	ENSOCUG00000003726	1 retrocopy	retro_ocun_120,
Otolemur garnettii	ENSOGAG00000001679	4 retrocopies	retro_ogar_1235, retro_ogar_1383, retro_ogar_2353, retro_ogar_981,
Procavia capensis	ENSPCAG00000005976	1 retrocopy	retro_pcap_241,
Pongo abelii	ENSPPYG00000012667	1 retrocopy	retro_pabe_391,
Pan troglodytes	ENSPTRG00000011637	1 retrocopy	retro_ptro_231,
Sorex araneus	ENSSARG00000009799	1 retrocopy	retro_sara_735,
Tarsius syrichta	ENSTSYG00000014537	1 retrocopy	retro_tsyr_225,
Tursiops truncatus	ENSTTRG00000000859	1 retrocopy	retro_ttru_712,