RetrogeneDB ID: retro_cjac_1183

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:8057456..8058598(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLF3
• Ensembl ID: ENSCJAG00000014163
• Aliases: None
• Description: None

Sequence

>retro_cjac_1183
GAGATCAATGAGAGTGCATCACAGACAAGGGATATTCTCAAACAACATTTTAATGATTTAAAGGGAACTCTCGGGAAGCT
CCTGGATGAGCAATTGGTGACCCTTTTGCAACCAGTGGACACTACAGAATGTACCATTAAGCCATTAGATGATTGCCAGA
AGCTCATAAAACAGGGAGTCAACACTCCAGTGGACTTAGTCGGAGAAGGTGATATTGCCATGCTTAGTGATGTAGGAGAA
AAGAATGAGAAACTGTGGAGCTTTACCAAAAAGGCCTTGCATGCTTAGTTGGAAAGCATACCAGAAGTACCTTTACTGGT
TGATGTGCCTTGTTTATCTGCTCCTTTGGATGATTCAATTCTTAGCATAATAAAAGACCACATTCTTAAGCATGAAACTG
TAGCATCTCACCCACCAGTACAGATAGAAGAACTGGTAGAGAAACCTGGAGCCATCATAGTATGATGGTGTAAGGTGGAT
GATGACTTTACAGCACAAGATTGTAGGCTCCAGTTTTGTAAATGTTCTTTAAATCATTTTAAAGACATATATGAAGCTTC
TGAAATGAATACATAGTATTGCACATAGACTCCAACGTTGATATCAGTTCAGAATCTTCACCTGAAGAGATGGCCGACAG
GCACAGAGTCCTTGGAGGATCCCCCAGATAATTCATTCCACATTAGTGCCTCATGAGTGGATAGCTGGTTTTGAGGGCTG
CAGTCTTAGAAATTGAAGAAATTTCTGGAATGATTCTGAATCTTGGGGTATTCCCTACTCCAGAATTCCAACTTATTTCA
GTGGGCAGGCATTAATATTTAGAGTTGAAACTGTGCGAGTACCAGACATAAGAGACAGTATAGGAGTGTGTCATAAAAAC
AGAATGGCTAGAACTCTCTGCAGCAGGATAAAGCTGTGTGTATTGGTACAAATGGTGCAGTTTTTGTAAATGGAAAAGAA
ATGTCTCATCAGTTACCCACAATTACTTCTGAGTCCACATTCACATTTGACATTGAGGCTGTGACTCTAAGAACCACCAA
TAATAATGAAGGCAGAAACGTCAAGCTCGAGTAACTCTTAGTTCAAATAACAGAGAAGTGGTTTCTGATTCGTTACTTGA
TTAATTTTGTGGTTCTCTTTAC

Alignment

ORF - retro_cjac_1183 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.04 %
• Parental protein coverage: 87.1 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QIKESASQTRDVLKQHFNDLKGTLGKLLDERLVTLLQEVDTIEQETIKPLDDCQKLIEHGVTTAEDLVRE
          .I.ESASQTRD.LKQHFNDLKGTLGKLLDE.LVTLLQ.VDT.E..TIKPLDDCQKLI..GV.T..DLV.E
Retrocopy EINESASQTRDILKQHFNDLKGTLGKLLDEQLVTLLQPVDTTEC-TIKPLDDCQKLIKQGVNTPVDLVGE

Parental  GEIAMLDGVGEENEKLWSFTKKASHIQLDSLPEVPLLVDVPCLSAQLDDSILNIVKDHIFKHGTVASRPP
          G.IAML..VGE.NEKLWSFTKKA.H..L.S.PEVPLLVDVPCLSA.LDDSIL.I.KDHI.KH.TVAS.PP
Retrocopy GDIAMLSDVGEKNEKLWSFTKKALHA*LESIPEVPLLVDVPCLSAPLDDSILSIIKDHILKHETVASHPP

Parental  VQIEELIEKPGGIIVRWCKVDDDFTAQDYRLQFRKSTSNHFEDVYVGSE-TEFIVLHIDPNVD-YQFRVC
          VQIEEL.EKPG.IIV.WCKVDDDFTAQD.RLQF.K...NHF.D.Y..SE..E.IVLHID.NVD.YQFR..
Retrocopy VQIEELVEKPGAIIV*WCKVDDDFTAQDCRLQFCKCSLNHFKDIYEASE<NEYIVLHIDSNVD<YQFRIF

Parental  ARGDGRQEWSPWSVPQIGHSTLVPHEWTAGFEGYSLSSRRNIALRNDSESSGVLYSRAPTYFCGQTLTFR
          ...DGRQ..SPW..PQI.HSTLVPHEW.AGFEG.SL...RN....NDSES.G..YSR.PTYF.GQ.L.FR
Retrocopy T*RDGRQAQSPWRIPQIIHSTLVPHEWIAGFEGCSLRN*RN--FWNDSESWGIPYSRIPTYFSGQALIFR

Parental  VETVGQPDRRDSIGVCAE-KQDGYDSLQRDQAVCISTNGTVFVNGKEMTNQLPAVTSGSTVTFDIEAVTL
          VETV..PD.RDSIGVC...KQ.G..SLQ.D.AVCI.TNG.VFVNGKEM..QLP..TS.ST.TFDIEAVTL
Retrocopy VETVRVPDIRDSIGVCHK<KQNG*NSLQQDKAVCIGTNGAVFVNGKEMSHQLPTITSESTFTFDIEAVTL

Parental  GTTNNSEGGNFKL-RVTISSNNREVVFDWLLDQSCGSLY
          .TTNN.EG.N.KL.RVT.SSNNREVV.D.LLD..CGSLY
Retrocopy RTTNNNEGRNVKL<RVTLSSNNREVVSDSLLD*FCGSLY

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	6.01 RPM
SRP051959_heart	0.00 RPM	12.16 RPM
SRP051959_kidney	0.00 RPM	4.90 RPM
SRP051959_liver	0.00 RPM	4.07 RPM
SRP051959_lung	0.00 RPM	11.81 RPM
SRP051959_lymph_node	0.00 RPM	21.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.56 RPM
SRP051959_spleen	0.00 RPM	10.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1183 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1183 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1183 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014163	1 retrocopy	retro_cjac_1183 ,
Homo sapiens	ENSG00000176390	3 retrocopies	retro_hsap_2121, retro_hsap_2133, retro_hsap_3360,
Gorilla gorilla	ENSGGOG00000005002	3 retrocopies	retro_ggor_1644, retro_ggor_1649, retro_ggor_2278,
Macaca mulatta	ENSMMUG00000009069	2 retrocopies	retro_mmul_1002, retro_mmul_998,
Mus musculus	ENSMUSG00000017561	1 retrocopy	retro_mmus_368,
Nomascus leucogenys	ENSNLEG00000005850	4 retrocopies	retro_nleu_1957, retro_nleu_2534, retro_nleu_2899, retro_nleu_2900,
Pongo abelii	ENSPPYG00000008142	3 retrocopies	retro_pabe_1925, retro_pabe_1984, retro_pabe_2672,
Pan troglodytes	ENSPTRG00000008963	2 retrocopies	retro_ptro_1560, retro_ptro_2175,