RetrogeneDB ID: retro_cjac_828

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:9958181..9959540(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000012436
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_828
GTGGCATCCTCCGAGGTGGCGCGGCACTTGCTCTTTCAGTCTCACATGGCAACGAAAACAACTTGTATGTCTTCACAAGA
ATCTGATGATGAACAGAGAAAAAGAGAAAACATTCGTTCCTTGACTCTGTCTGGCCGTGTTGGTTTTGAGAGTTTGCCTG
ATCAGCTGGTGAACAGATCCATTCAGCAAGGTTTCTGCTTTAATATTCTCTGCGTGGGGGAAACTGGAATTGGAAAATCA
ACACTGATTAACACATTGTTTAATACTAATTTTGAAGACCATGAACACTCACATTTTTGCCCAAATGTTAAACTTAAAGC
TCAGACATATGAACTCCAGGAAGGTAATGTTCGATTGAAATTGACCATTGTGAATACAGTGGGATTTGGTGACCAAATCA
ATAAAGAAGAGAGCTACCAACCGATAGTTGACTACATCGATGCTCAGTTTGAGGCCTACCTCCAAGAAGAACTGAAGATT
AAGCGTTCTCTCTTTACCTGCCGTGATTCTCGCGTCCATGTGTGCCTCTACTTCATTTCACCGACTGGCCACTCTCTGAA
GACACTTGATCTCTTAACCATGAAGCACCTTGACAGCAAGGTAAACGTTATACCAGTGATTGCCAAAGCAGATACGGTTT
CTAAAACTGAATTACAGAAGTTTAAGATCAAGCTCATGAGTGAATGGGTCAGCAGTGGCATCCAGATATACCAGTTCCCA
ACAGATGATGACACTGTTGCTAAGATCAATGCTGCGATGAATGGACAGTTGCCGTTTGCCGTCGTGGGAAGTACGGATGA
GGTGAAAGTTGGAAACAAGATGGTCAAAGCTCGCCAGTACCCTTGGGGTGTTGTACAAGTGGAAAATGAAAACCACTGTG
ACTTTGTGAAGCTGCGGGAAATGCTCATTTCTACAAACATGGAGGACCTGCGAGAACAGACCCATACCAGGCACTATGAG
CTTTACAGGCGCTGCAAACTGGAGGAAATGGGCTTTACAGACGTGGGCCCAGAGAACAAGCCGGTCAGTCTTCAAGACAC
CTATGAAGCCAAACGACATGAGTTTCATGGTGAACGTCAGAGGAAGGAAGAAAAAATGAAGGAGATGTTTGTGAAGCGAG
TAAAGGAGAAAGAAGCCACATTGAAAGTAGCTGAGAGAGAGCTACAGGCCAAAGCTGAGCACCTTCAGAGACTTCACCAA
GAAGAGAGCATGAAGCTCGAAGAAAAGAGAAGACTTTTGGAAGAAGAAATCATTGCTTTCTCTAAAAAGAAAGCTACCTC
TGAGATATTCCACAACCAGTCCTTCCTGGCAACAGGCAGCGATCTGTGGAAGGACAAGGACAGTAAGAACTCCAATTTT

Alignment

ORF - retro_cjac_828 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.16 %
• Parental protein coverage: 99.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASSEVARHLLFQSHMATKTTCMSSQESDDEQRKRENIRSLTMSGHVGFESLPDQLVNRSIQQGFCFNIL
          .ASSEVARHLLFQSHMATKTTCMSSQESDDEQRKRENIRSLT.SG.VGFESLPDQLVNRSIQQGFCFNIL
Retrocopy VASSEVARHLLFQSHMATKTTCMSSQESDDEQRKRENIRSLTLSGRVGFESLPDQLVNRSIQQGFCFNIL

Parental  CVGETGIGKSTLIDTLFNTNFKDHESSHFCPNVKLKAQTYELQESNVRLKLTIVNTVGFGDQINKEESYQ
          CVGETGIGKSTLI.TLFNTNF.DHE.SHFCPNVKLKAQTYELQE.NVRLKLTIVNTVGFGDQINKEESYQ
Retrocopy CVGETGIGKSTLINTLFNTNFEDHEHSHFCPNVKLKAQTYELQEGNVRLKLTIVNTVGFGDQINKEESYQ

Parental  PIVDYIDAQFEAYLQEELKIKRSLFTYHDSRIHVCLYFISPTGHSLKTLDLLTMKNLDSKVNIIPVIAKA
          PIVDYIDAQFEAYLQEELKIKRSLFT..DSR.HVCLYFISPTGHSLKTLDLLTMK.LDSKVN.IPVIAKA
Retrocopy PIVDYIDAQFEAYLQEELKIKRSLFTCRDSRVHVCLYFISPTGHSLKTLDLLTMKHLDSKVNVIPVIAKA

Parental  DTVSKTELQKFKIKLMSELVSNGVQIYQFPTDDDTIAKINAAMNGQLPFAVVGSMDEVKVGNKMVKARQY
          DTVSKTELQKFKIKLMSE.VS.G.QIYQFPTDDDT.AKINAAMNGQLPFAVVGS.DEVKVGNKMVKARQY
Retrocopy DTVSKTELQKFKIKLMSEWVSSGIQIYQFPTDDDTVAKINAAMNGQLPFAVVGSTDEVKVGNKMVKARQY

Parental  PWGVVQVENENHCDFVKLREMLISTNMEDLREQTHTRHYELYRRCKLEEMGFTDVGPENKPVSLQETYEA
          PWGVVQVENENHCDFVKLREMLISTNMEDLREQTHTRHYELYRRCKLEEMGFTDVGPENKPVSLQ.TYEA
Retrocopy PWGVVQVENENHCDFVKLREMLISTNMEDLREQTHTRHYELYRRCKLEEMGFTDVGPENKPVSLQDTYEA

Parental  KRHEFHGERQRKEEEMKQMFVQRVKEKEAILKEAERELQAKFEHLKRLHQEERMKLEEKRRLLEEEIIAF
          KRHEFHGERQRKEE.MK.MFV.RVKEKEA.LK.AERELQAK.EHL.RLHQEE.MKLEEKRRLLEEEIIAF
Retrocopy KRHEFHGERQRKEEKMKEMFVKRVKEKEATLKVAERELQAKAEHLQRLHQEESMKLEEKRRLLEEEIIAF

Parental  SKKKATSETSHNQSFLATGSNLRKDKDRKNSNF
          SKKKATSE..HNQSFLATGS.L.KDKD.KNSNF
Retrocopy SKKKATSEIFHNQSFLATGSDLWKDKDSKNSNF

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	26.49 RPM
SRP051959_heart	0.00 RPM	21.19 RPM
SRP051959_kidney	0.02 RPM	33.10 RPM
SRP051959_liver	0.04 RPM	39.12 RPM
SRP051959_lung	0.05 RPM	25.52 RPM
SRP051959_lymph_node	0.00 RPM	7.60 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.26 RPM
SRP051959_spleen	0.00 RPM	20.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_828 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_828 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_828 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,