RetrogeneDB ID: retro_cjac_2035

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:46660286..46660878(+)
• Located in intron of: ENSCJAG00000015729

Retrocopy information

• Ensembl ID: ENSCJAG00000015777
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TAGLN2
• Ensembl ID: ENSCJAG00000006156
• Aliases: None
• Description: transgelin 2 [Source:HGNC Symbol;Acc:11554]

Sequence

>retro_cjac_2035
CTCTCCAGCCCGCTCGAACGCTCCCCACAGCCACTGCCACCCACTGGAATGGCCAACAGGGGACCTGCATATGGCCTGAG
CCGGGAGGTGCAGCAGAACATTGAAAAGCAACACGACGCAGACCTGGAGCAGATCCTGATCCAGTGGATCACCACCCAGT
GCCCAAAGGATGTGGGCCGGCCCCAGCCTGGGTGGGAGAACTTCCAGAACTGGCTCAAGGATGGCACGGTGCTATGTGAG
CTCATTAATGCACTGCACCCGAGGGGCAGGCCCCTGTAAAGAAGATCCAGGCCTCCACCATGGCCTTCAAGCAGACGGAG
CAGAGGTCTCAGTTCCTGCAGGCAGCTGAGGGCTGTGGCATTAGCACCGCCGACATCTTCCAAACCGTGGACCTCTGGGA
AGGAAAGAACATGGCCTGTGTGCAGCAGACACTGATGAATCTGGGTGGCTGGCGGTAGCCCAGGATGATGGGCTCTTCTC
TGGGGATCCCAATTGGTTCCCTAAGAAATCCAAGGAGAATCCTCGGAACTTCTCGGACAACCAGCTGCAAGAGGGCAGGA
ACGTGATCAGGTTACAGATGGGCACCAACCGC

Alignment

ORF - retro_cjac_2035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88. %
• Parental protein coverage: 90. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LALALVSSPQPPPPIGMANRGPAYGLSREVQQKIEKQYDADLEQILIQWITTQCRKDVGRPQPGRENFQN
          L...L..SPQP.PP.GMANRGPAYGLSREVQQ.IEKQ.DADLEQILIQWITTQC.KDVGRPQPG.ENFQN
Retrocopy LSSPLERSPQPLPPTGMANRGPAYGLSREVQQNIEKQHDADLEQILIQWITTQCPKDVGRPQPGWENFQN

Parental  WLKDGTVLCELINALY-PEGQAPVKKIQASAMAFKQMEQISQFLQAAERYGINTTDIFQTVDLWEGKNMA
          WLKDGTVLCELINAL..PEGQAPVKKIQAS.MAFKQ.EQ.SQFLQAAE..GI.T.DIFQTVDLWEGKNMA
Retrocopy WLKDGTVLCELINALH<PEGQAPVKKIQASTMAFKQTEQRSQFLQAAEGCGISTADIFQTVDLWEGKNMA

Parental  CVQRTLMNLGG-LAVARDDGLFSGDPNWFPKKSKENPRNFSDNQLQEGRNVIGLQMGTNR
          CVQ.TLMNLGG.LAVA.DDGLFSGDPNWFPKKSKENPRNFSDNQLQEGRNVI.LQMGTNR
Retrocopy CVQQTLMNLGG<LAVAQDDGLFSGDPNWFPKKSKENPRNFSDNQLQEGRNVIRLQMGTNR

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	1.29 RPM	62.35 RPM
SRP051959_heart	0.05 RPM	31.41 RPM
SRP051959_kidney	0.22 RPM	21.17 RPM
SRP051959_liver	0.02 RPM	10.96 RPM
SRP051959_lung	0.23 RPM	86.17 RPM
SRP051959_lymph_node	0.02 RPM	34.09 RPM
SRP051959_skeletal_muscle	0.02 RPM	15.09 RPM
SRP051959_spleen	0.08 RPM	32.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2035 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2035 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2035 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002068	1 retrocopy	retro_btau_1701,
Callithrix jacchus	ENSCJAG00000005530	1 retrocopy	retro_cjac_681,
Callithrix jacchus	ENSCJAG00000006156	2 retrocopies	retro_cjac_2035 , retro_cjac_2444,
Callithrix jacchus	ENSCJAG00000012755	2 retrocopies	retro_cjac_723, retro_cjac_778,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Homo sapiens	ENSG00000158710	1 retrocopy	retro_hsap_4108,
Macropus eugenii	ENSMEUG00000006573	9 retrocopies	retro_meug_1092, retro_meug_1242, retro_meug_128, retro_meug_1442, retro_meug_1998, retro_meug_309, retro_meug_483, retro_meug_690, retro_meug_880,
Myotis lucifugus	ENSMLUG00000026228	1 retrocopy	retro_mluc_274,
Macaca mulatta	ENSMMUG00000004705	1 retrocopy	retro_mmul_2328,
Monodelphis domestica	ENSMODG00000010032	1 retrocopy	retro_mdom_1178,
Nomascus leucogenys	ENSNLEG00000013350	1 retrocopy	retro_nleu_575,
Pongo abelii	ENSPPYG00000000648	2 retrocopies	retro_pabe_3310, retro_pabe_3364,
Pan troglodytes	ENSPTRG00000001533	1 retrocopy	retro_ptro_2788,
Sus scrofa	ENSSSCG00000006395	2 retrocopies	retro_sscr_312, retro_sscr_313,
Tarsius syrichta	ENSTSYG00000001645	2 retrocopies	retro_tsyr_1911, retro_tsyr_950,
Tursiops truncatus	ENSTTRG00000001814	1 retrocopy	retro_ttru_1614,