RetrogeneDB ID: retro_cjac_1736

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:18978579..18979930(-)
• Located in intron of: ENSCJAG00000004852

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SEPT10
• Ensembl ID: ENSCJAG00000017754
• Aliases: None
• Description: septin 10 [Source:HGNC Symbol;Acc:14349]

Sequence

>retro_cjac_1736
ATGGCATCCTCCAAGGTGGCGCAGCACTTGCTCTTTCAGTCTCACATGGCAACGAAAACAACTTGTATGTTTTCACAAGG
ATCTGATGATGAACAGAGAAAAAAAGAAAACATTCGTTCCTTGACTATGTCTGGGCCCGTTGGTTTTGAGAGTTTGCTTG
ATCAGCTGGTGAACAGATCCATTCAGCAAGGTTTCTGCTTTCATATTCTCTGCGTGGGGGAAACTGGAGTTGGAAAATCA
ACACTGATTGACACATAGTTTAATACTAATTTTGAAGACCATAAATCCTCACATTTTTGCCCAAATGTTAAACTTAAAGC
TCAGACATATGAACTCCAGGAAAGTAATGGTCGATTGAAATTGACCATTGTGAATACAGTGGGATTCAGTGACCAAATAA
ATAAAGAAGAGAGCTACCAACCAGTAGTTGACTACATAGATGCTCAGTTTGAGGCCTGTCTCCAAGAAGAACTGAAGATT
AAGTGTTCTCTCTTGACCTACCATGATTCTCGCCTCCATGTCTGCCTCTACTTCATTTCACCGACCGGCCTCTCTCTGAA
GACACTTGATCTCTTAACCATGAAGAACCTTGACAGCGAGGTAAACATTATACCAGTGATTGCCAAATCAGATACGGTTT
CTAAAACTGAATTACAGAAATTTAAGAACAAGCTCATGAGTGAGTTGGTCAGCAGTGGCATCCAGATATACCAGTTCCCA
ACAGATGATGACACTGTTGCTAAGATCAATGCTGCGATGAATGGACAGTTGCCATTTGCTGTTGTGGGAAGTATGGATGA
GGTAAAAGTCAGAGACAAGATGGTCAAAGCTCACCAGTACCCTTTGGGTGTTGTACAAGTGGAAAATGAAAACCACCGTG
ACTTTGTAAAGCTGCAGGAAATGCTCATTTATACAAACATGGAGGACCTGCAAGAGCAAACCCATACCAGGCACTATGAG
CTTTATAGGCACTGCAAACTGGAGGAAATGGGCTTTACAGATGTGGGCCCAGAGAACAAGCCGGTCAGTCTTCAAGAGAC
CTACGAAGCCAAAAGACATGAGTTTCATGGTGAACATCAGAGGAAGAAAGAAGAAATGAAGCAGATGTTTGTGCAGTGAG
TAAAGGAGAAAGAAGCCATATTGAAAGAAGCTGAGAGAGAGCTACAGGCCAAATTTGAGCACCTTAAGAGACTTCACCAA
GAAGAGAGAATGAAGCTTGAAGAAAAGAGAAGACTTTTGGAAGAAGAAATAATTGCTTTCTCTAAAAAGAAAGCTACCTC
CCAAGATATTTCACAGCCAGTCCTTTTTGGCAACAGGCAGCAATCTGAGGAAGGACAAGGACCGTAGCAGT

Alignment

ORF - retro_cjac_1736 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.02 %
• Parental protein coverage: 99.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASSEVARHLLFQSHMATKTTCMSSQESDDEQRKRENIRSLTMSGHVGFESLPDQLVNRSIQQGFCFNIL
          MASS.VA.HLLFQSHMATKTTCM.SQ.SDDEQRK.ENIRSLTMSG.VGFESL.DQLVNRSIQQGFCF.IL
Retrocopy MASSKVAQHLLFQSHMATKTTCMFSQGSDDEQRKKENIRSLTMSGPVGFESLLDQLVNRSIQQGFCFHIL

Parental  CVGETGIGKSTLIDTLFNTNFKDHESSHFCPNVKLKAQTYELQESNVRLKLTIVNTVGFGDQINKEESYQ
          CVGETG.GKSTLIDT.FNTNF.DH.SSHFCPNVKLKAQTYELQESN.RLKLTIVNTVGF.DQINKEESYQ
Retrocopy CVGETGVGKSTLIDT*FNTNFEDHKSSHFCPNVKLKAQTYELQESNGRLKLTIVNTVGFSDQINKEESYQ

Parental  PIVDYIDAQFEAYLQEELKIKRSLFTYHDSRIHVCLYFISPTGHSLKTLDLLTMKNLDSKVNIIPVIAKA
          P.VDYIDAQFEA.LQEELKIK.SL.TYHDSR.HVCLYFISPTG.SLKTLDLLTMKNLDS.VNIIPVIAK.
Retrocopy PVVDYIDAQFEACLQEELKIKCSLLTYHDSRLHVCLYFISPTGLSLKTLDLLTMKNLDSEVNIIPVIAKS

Parental  DTVSKTELQKFKIKLMSELVSNGVQIYQFPTDDDTIAKINAAMNGQLPFAVVGSMDEVKVGNKMVKARQY
          DTVSKTELQKFK.KLMSELVS.G.QIYQFPTDDDT.AKINAAMNGQLPFAVVGSMDEVKV..KMVKA.QY
Retrocopy DTVSKTELQKFKNKLMSELVSSGIQIYQFPTDDDTVAKINAAMNGQLPFAVVGSMDEVKVRDKMVKAHQY

Parental  PWGVVQVENENHCDFVKLREMLISTNMEDLREQTHTRHYELYRRCKLEEMGFTDVGPENKPVSLQETYEA
          P.GVVQVENENH.DFVKL.EMLI.TNMEDL.EQTHTRHYELYR.CKLEEMGFTDVGPENKPVSLQETYEA
Retrocopy PLGVVQVENENHRDFVKLQEMLIYTNMEDLQEQTHTRHYELYRHCKLEEMGFTDVGPENKPVSLQETYEA

Parental  KRHEFHGERQRKEEEMKQMFVQRVKEKEAILKEAERELQAKFEHLKRLHQEERMKLEEKRRLLEEEIIAF
          KRHEFHGE.QRK.EEMKQMFVQ.VKEKEAILKEAERELQAKFEHLKRLHQEERMKLEEKRRLLEEEIIAF
Retrocopy KRHEFHGEHQRKKEEMKQMFVQ*VKEKEAILKEAERELQAKFEHLKRLHQEERMKLEEKRRLLEEEIIAF

Parental  SKKKATSE-TSHNQSFLATGSNLRKDKDRKN
          SKKKATS....H.QSFLATGSNLRKDKDR..
Retrocopy SKKKATSQ>IFHSQSFLATGSNLRKDKDRSS

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	1.73 RPM	26.49 RPM
SRP051959_heart	1.12 RPM	21.19 RPM
SRP051959_kidney	1.26 RPM	33.10 RPM
SRP051959_liver	0.69 RPM	39.12 RPM
SRP051959_lung	1.17 RPM	25.52 RPM
SRP051959_lymph_node	1.80 RPM	7.60 RPM
SRP051959_skeletal_muscle	0.28 RPM	9.26 RPM
SRP051959_spleen	1.76 RPM	20.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1736 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1736 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1736 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006122	1 retrocopy	retro_cjac_1501,
Callithrix jacchus	ENSCJAG00000012276	2 retrocopies	retro_cjac_1259, retro_cjac_3809,
Callithrix jacchus	ENSCJAG00000014744	1 retrocopy	retro_cjac_2336,
Callithrix jacchus	ENSCJAG00000017754	3 retrocopies	retro_cjac_1736 , retro_cjac_2879, retro_cjac_828,
Homo sapiens	ENSG00000186522	1 retrocopy	retro_hsap_4060,
Gorilla gorilla	ENSGGOG00000013659	1 retrocopy	retro_ggor_2728,
Myotis lucifugus	ENSMLUG00000017273	1 retrocopy	retro_mluc_2285,
Nomascus leucogenys	ENSNLEG00000001328	1 retrocopy	retro_nleu_2111,
Pongo abelii	ENSPPYG00000012144	1 retrocopy	retro_pabe_3335,