RetrogeneDB ID: retro_cjac_1571

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:68473777..68474826(+)
• Located in intron of: ENSCJAG00000012734

Retrocopy information

• Ensembl ID: ENSCJAG00000012749
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_1571
ATGGCGGTGCCCACTGCACCCACGGGGCCCTCGGCATTGGGCCAGACCGGCCCCGGCTGGCCCTGCGGTACTCAGTGAGC
AGCGGCCCGTCCCGCTACGTGCTTGGGATGCAGGAGCTGTTTCGGGGCCACAGCAAGACGCGCGAGTTACTGGCGCACAG
CGCCAAGGTGCACTCTGTGGCCTGGAGCTGCGACGGGCGTCGCCTAGCCTCGGGGTCCTTCGACAAGACGGCCAGCGTCT
TCTTGCTGGAGAAGGACCGGCTGGTCAAAGAAAACAATTATCGGGGACATGGAGATAGTGTGGACCAGCTTTGTTGGCAT
CCAAGTAATCCTGACCTATTTGTTACGGCATCTGGAGATAAAACCATTCGCATCTGGGATGTGAGGACTACAAAATGCAT
GGCCACTGTGAACACTAAAGGGGAGAACATTAATATCTGCTGGAGTCCTGATGGGCAGACCATTGCTGTAGGCAACAAGG
ATGATGTGGGGACTTTCATCGATGCCAAGACACACCGTTCCAAAGCAGAAGAGCAGTTCAAGTTTGAGGTCAATGAAATC
TCCTGGAACAATGACAATAACATGTTCTTCCTGACAAACGGCAATGGTTGTATCAACATCCTCAGTTACCCAGAACTGAA
GCCTGTGCAGTCCATCAACGCCCATCCTTCCAACTGCATCTGTATCAAGTTTGACCCCATGGGGAAGTACTTTGCCACAG
GAAGTGCAGATGCTTTGGTTAGCCTCTGGGATGTGGACGAGTTAGTGTGTGTTCGGTGCTTTTCCAGGCTGGATTGGCCT
GTAAGGACTCTCAGTTTCAGCCACGATGGGAAAATGCTGGCGTCAGCATCGGAAGATCATTTTATTGACATTGCTGAAGT
GGAGACAGGGGACAAGCTATGGGAGGTACAGTGTGAGTCTCCAACCTTCCTGGTGGCGTGGCACCCTAAAAGGCCTCTGC
TGGCATTTGCCTGTGATGGCAAAGATGGCAAATATGACAGTAGCCGGGAAGCTGGAACTGTGAAGCTGTTTGGGCTTCCT
AATGATTCT

Alignment

ORF - retro_cjac_1571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVPTAPMGPSA-LGQTGPGSMASWCSVSSGPSRYVLGMQELFRGHSKTREFLAHSAKVHSVAWSCDGRR
          MAVPTAP.GPSA..G...P...A...SVSSGPSRYVLGMQELFRGHSKTRE.LAHSAKVHSVAWSCDGRR
Retrocopy MAVPTAPTGPSA<IGPDRP-RLALRYSVSSGPSRYVLGMQELFRGHSKTRELLAHSAKVHSVAWSCDGRR

Parental  LASGSFDKTASVFLLEKDRLVKENNYRGHGDSVDQLCWHPSNPDLFVTASGDKTIRIWDVRTTKCIATVN
          LASGSFDKTASVFLLEKDRLVKENNYRGHGDSVDQLCWHPSNPDLFVTASGDKTIRIWDVRTTKC.ATVN
Retrocopy LASGSFDKTASVFLLEKDRLVKENNYRGHGDSVDQLCWHPSNPDLFVTASGDKTIRIWDVRTTKCMATVN

Parental  TKGENINICWSPDGQTIAVGNKDDVVTFIDAKTHRSKAEEQFKFEVNEISWNNDNNMFFLTNGNGCINIL
          TKGENINICWSPDGQTIAVGNKDDV.TFIDAKTHRSKAEEQFKFEVNEISWNNDNNMFFLTNGNGCINIL
Retrocopy TKGENINICWSPDGQTIAVGNKDDVGTFIDAKTHRSKAEEQFKFEVNEISWNNDNNMFFLTNGNGCINIL

Parental  SYPELKPVQSINAHPSNCICIKFDPMGKYFATGSADALVSLWDVDELVCVRCFSRLDWPVRTVSFSHDGK
          SYPELKPVQSINAHPSNCICIKFDPMGKYFATGSADALVSLWDVDELVCVRCFSRLDWPVRT.SFSHDGK
Retrocopy SYPELKPVQSINAHPSNCICIKFDPMGKYFATGSADALVSLWDVDELVCVRCFSRLDWPVRTLSFSHDGK

Parental  MLASASEDHFIDIAEVETGDKLWEVQCESPTFTVAWHPKRPLLAFACDDKDGKYDSSREAGTVKLFGLPN
          MLASASEDHFIDIAEVETGDKLWEVQCESPTF.VAWHPKRPLLAFACD.KDGKYDSSREAGTVKLFGLPN
Retrocopy MLASASEDHFIDIAEVETGDKLWEVQCESPTFLVAWHPKRPLLAFACDGKDGKYDSSREAGTVKLFGLPN

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	2.13 RPM	7.17 RPM
SRP051959_heart	1.61 RPM	5.70 RPM
SRP051959_kidney	2.13 RPM	7.81 RPM
SRP051959_liver	2.51 RPM	10.18 RPM
SRP051959_lung	2.05 RPM	5.53 RPM
SRP051959_lymph_node	0.96 RPM	5.30 RPM
SRP051959_skeletal_muscle	1.40 RPM	5.92 RPM
SRP051959_spleen	1.95 RPM	5.88 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1571 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1571 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,