RetrogeneDB ID: retro_cjac_3072

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:52544166..52545215(+)
• Located in intron of: ENSCJAG00000013400

Retrocopy information

• Ensembl ID: ENSCJAG00000013420
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: THOC3
• Ensembl ID: ENSCJAG00000006495
• Aliases: None
• Description: None

Sequence

>retro_cjac_3072
TTGGCGGTGCCCACTGCACCCATGGGGCCCTCGGCTTTGGGCCAGACCAGCCCCGGCTGGCCCCGTGGTGCTCAGTGAGC
AGTGGCCCGTCGCGCTACGTGCTTGGGATGCAGGAGCTGTTCCGGGGCCACAGCAAGACGCGTGAATTCCTGGCGCACAG
CGCCAAGGTGCACTCGGTGGCCTGGAGCTGTGACGGGCGTCACCTAGCCTCGGGGTCCTTCGACAAGACGGCCAGCGTCT
TCTTGCTGGAGAAGGACCGGTTGGTCAAAGAAAATAATTATCGGGGACATGGAGATAGTGTGGACCAGCTTTGTTGGCAT
CCAAGTAATCCTGACCTATTTGTTACGGCATCTGGAGATAAAACCATTCGCATCTGGGATGTGAGGACTACAAAATGCAT
TGCCACTGTGAACATTAAAGGGGAGAACATTAATGTCTGCTGGAGTCCTGATGGGCAGACCATTGCTGTAGGCAACAAGG
ATGACGTGGTGACTTTCATCGATGCCAAGACACACCGTTCCAAAGCAGAAGAGCAGTTCAAGTTTGAGGTCAATGAAATC
TCCTGGAACAATGACAATAACATGTTCTTCCTGACAAATGGCAATGGTTGTATCAACATCCTCAGTTACCCGGAACTGAA
ACTTGTGCAGTCCATCAACGCCCATCCTTCCAACTGCATCTGTATCAAGTTTGACCCCATGGAGAAGTACTTTGCCACAG
GAAGTGCAGATGCTTTGGTTAGCCTCTGGGATGTGGACGAGTTAGTGGGTGTTCGGTGCTTTTCCAGGCTGGATTGGCCT
GTAAGGACTCTCAGTTTCAGCCACGATGGGAAAATGCTGGCGTCAGCATCAGAAGATCATTTTATTGACATCACTGAAGT
GGAGACAGGGGACAAGCTATGGGAGGTACAGTGTGAGTCTCCGACCTTCACCGTGGCATGGCACCCCAAAAGGCCTCTGC
TGGCATTTGCCTGTGATGGCAAAGACGGCAAATATGACAGTAGCCAGGAAGCCGGAACTGTGAAGCTGTTTGGGCTTTCT
AATGATTCT

Alignment

ORF - retro_cjac_3072 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVPTAPMGPSAL-GQTGPGSMASWCSVSSGPSRYVLGMQELFRGHSKTREFLAHSAKVHSVAWSCDGRR
          .AVPTAPMGPSAL.G...P...A.WCSVSSGPSRYVLGMQELFRGHSKTREFLAHSAKVHSVAWSCDGR.
Retrocopy LAVPTAPMGPSAL<GPDQP-RLAPWCSVSSGPSRYVLGMQELFRGHSKTREFLAHSAKVHSVAWSCDGRH

Parental  LASGSFDKTASVFLLEKDRLVKENNYRGHGDSVDQLCWHPSNPDLFVTASGDKTIRIWDVRTTKCIATVN
          LASGSFDKTASVFLLEKDRLVKENNYRGHGDSVDQLCWHPSNPDLFVTASGDKTIRIWDVRTTKCIATVN
Retrocopy LASGSFDKTASVFLLEKDRLVKENNYRGHGDSVDQLCWHPSNPDLFVTASGDKTIRIWDVRTTKCIATVN

Parental  TKGENINICWSPDGQTIAVGNKDDVVTFIDAKTHRSKAEEQFKFEVNEISWNNDNNMFFLTNGNGCINIL
          .KGENIN.CWSPDGQTIAVGNKDDVVTFIDAKTHRSKAEEQFKFEVNEISWNNDNNMFFLTNGNGCINIL
Retrocopy IKGENINVCWSPDGQTIAVGNKDDVVTFIDAKTHRSKAEEQFKFEVNEISWNNDNNMFFLTNGNGCINIL

Parental  SYPELKPVQSINAHPSNCICIKFDPMGKYFATGSADALVSLWDVDELVCVRCFSRLDWPVRTVSFSHDGK
          SYPELK.VQSINAHPSNCICIKFDPM.KYFATGSADALVSLWDVDELV.VRCFSRLDWPVRT.SFSHDGK
Retrocopy SYPELKLVQSINAHPSNCICIKFDPMEKYFATGSADALVSLWDVDELVGVRCFSRLDWPVRTLSFSHDGK

Parental  MLASASEDHFIDIAEVETGDKLWEVQCESPTFTVAWHPKRPLLAFACDDKDGKYDSSREAGTVKLFGLPN
          MLASASEDHFIDI.EVETGDKLWEVQCESPTFTVAWHPKRPLLAFACD.KDGKYDSS.EAGTVKLFGL.N
Retrocopy MLASASEDHFIDITEVETGDKLWEVQCESPTFTVAWHPKRPLLAFACDGKDGKYDSSQEAGTVKLFGLSN

Parental  DS
          DS
Retrocopy DS

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	0.58 RPM	7.17 RPM
SRP051959_heart	0.60 RPM	5.70 RPM
SRP051959_kidney	0.42 RPM	7.81 RPM
SRP051959_liver	0.09 RPM	10.18 RPM
SRP051959_lung	0.98 RPM	5.53 RPM
SRP051959_lymph_node	0.05 RPM	5.30 RPM
SRP051959_skeletal_muscle	0.26 RPM	5.92 RPM
SRP051959_spleen	0.11 RPM	5.88 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3072 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3072 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3072 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006495	2 retrocopies	retro_cjac_1571, retro_cjac_3072 ,
Macropus eugenii	ENSMEUG00000001068	2 retrocopies	retro_meug_1061, retro_meug_19,
Monodelphis domestica	ENSMODG00000005339	1 retrocopy	retro_mdom_164,
Mus musculus	ENSMUSG00000025872	2 retrocopies	retro_mmus_1821, retro_mmus_441,
Otolemur garnettii	ENSOGAG00000003503	1 retrocopy	retro_ogar_3005,
Sarcophilus harrisii	ENSSHAG00000010757	1 retrocopy	retro_shar_4,