RetrogeneDB ID: retro_cjac_2217

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:26470478..26471957(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EML4
• Ensembl ID: ENSCJAG00000014719
• Aliases: None
• Description: None

Sequence

>retro_cjac_2217
ATGGACGGTTTTGCCGGCAGCCTCGATGATGACATTTCTGCTGCAAGTACTTCTGATGTTCAAGATCTCCTGTCAGCTCT
TGAGTCAGGAGTTCAGCAATAAGAAGATGAAATCACTGTGCTAAAGGTAACTTTGGCTGATGTTTTGAGGCGTATTGCAA
TCTCTGACGATCATGTGGCCTCAGTGAAAAAATCAGTCTCAAATAACGGCCAACCAAGCCCTGGAGCAGCTATTCCCGTG
TCCTGTCTAACCAATGCAAGTTGTGCAAACAGAAAACCAAGTCATATGATTGCTGTCTCAATTGCAGGAAAAGAAACTCT
TTCATCTGCTGCTAAAAGCATAAAACGACCATTGCCAGCTGCAAAGTCACATAATTCATGGGAAAATTCAGATAATAGCC
GTAATAAATTGTCGAAAATAACTTCAACACCCAAATTAATACCAAAAGTTACCAAAAATGCAGATAAGCATAAAGATGTC
ATCGTCAACCAAGAGGGAGAATATATTAAAATATTTATGCGAGTTCGGCCAATTACCACGTTCACTCCTTCTGATGTTGA
CAACCATGATGACATCAGAACAGAACTGCCTCCTGAGAAACTCAAACTGGAGTGGGCATATAGTTATGAGAAAAGGACTG
TAGAGCTAATGTTTACCTTCTTCCAACCAGGGAAATAGTTTATTTCATTGCACCAGTAGTAGTACTATTTAATTATCAAG
AGAGAGCTCAGCAACACTACCTGGGTCATACAGACTGTGTAAAATGCCTTGCTATCCATCCTGACAAAATTAGGATTGCA
ACTGGACAGATAGCTGGCGTGGATAAAGATAGAATGCCTCTACAACGCCACGTCAGAGCGTGGGATTCTGTTACTCATCT
ACACTGCAGATTAATGGAGTTGGCACTTTTGAGCATGGAGTAGGATGCCTGGATTTTTCAAAAGCAGATTCAGGTGTTCA
TTTATGTGTTATCGATGACTCCAATGAGTATATGCTTACTGTATGGGACTGGCAGAAAAAAGCAAAAGGAGCAGAAATAA
AGACAACAAACGAAGTTGTTTTGGCTGTAGAGTTTCACCCAACAGATGGGAATACCATAATAACACGCGGTAAATCTAAT
ATTTTCTTCTGGACCTGGAGTGGCAATCACTAACAAGAAAACAGGGAATTTGGGGGAAATATGGAAAGCAAAAATTTGTG
CAGTGTTTAGCATTCTTGGGGAATAGAGATGTTCTTACTGGAGACTCAGGTGGAGTCATGCTTCTATGGAACAAAACTCT
TCAGAGCCCATACCTGGGAGAGGTCCTAAAGGTGTATATCAAAGGGGCAAACAAATCAAAGCTACAATGGCCGTGTGTTC
ACACTTTATCAGCTGAGAAATGGGATGTTATTAACTGGAAGAGGGAAAGACAGAAAAATAATTCTGTGGGATCATGATCT
GAATCTGAAAGAGAAATAGAGGTTTCTGATCAGTATGGT

Alignment

ORF - retro_cjac_2217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.83 %
• Parental protein coverage: 53.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MDGFAGSLDDSISAASTSDVQDRLSALESRVQQQEDEITVLKAALADVLRRLAISEDHVASVKKSVSSKG
          MDGFAGSLDD.ISAASTSDVQD.LSALES.VQQ.EDEITVLK..LADVLRR.AIS.DHVASVKKSVS..G
Retrocopy MDGFAGSLDDDISAASTSDVQDLLSALESGVQQ*EDEITVLKVTLADVLRRIAISDDHVASVKKSVSNNG

Parental  QPSPRAAIPMSCITNGSGANRKPSQTSAVSIAGKETVSSAAKSIKRPSPAEKSHNSWENSDDSRNKLSKI
          QPSP.AAIP.SC.TN.S.ANRKPS...AVSIAGKET.SSAAKSIKRP.PA.KSHNSWENSD.SRNKLSKI
Retrocopy QPSPGAAIPVSCLTNASCANRKPSHMIAVSIAGKETLSSAAKSIKRPLPAAKSHNSWENSDNSRNKLSKI

Parental  PSTPKLIPKVTKNADKHKDVIINQEGEYIKMFMRGRPITMFIPSDVDNYDDIRTELPPEKLKLEWVYGYR
          .STPKLIPKVTKNADKHKDVI.NQEGEYIK.FMR.RPIT.F.PSDVDN.DDIRTELPPEKLKLEW.Y.Y.
Retrocopy TSTPKLIPKVTKNADKHKDVIVNQEGEYIKIFMRVRPITTFTPSDVDNHDDIRTELPPEKLKLEWAYSYE

Parental  -GKDCRANVYLLPTGEIVYFIASVVVLFNYEERTQRHYLGHTDCVKCLAIHPDKIRIATGQIAGVDKDGR
          ..KDCRANVYLLPT.EIVYFIA.VVVLFNY.ER.Q.HYLGHTDCVKCLAIHPDKIRIATGQIAGVDKD..
Retrocopy <EKDCRANVYLLPTREIVYFIAPVVVLFNYQERAQQHYLGHTDCVKCLAIHPDKIRIATGQIAGVDKDRM

Parental  PLQPHVRVWDSVT-LSTLQIIGLGTFERGVGCLDFSKADSGVHLCVIDDSNEHMLTVWDWQKKAKGAEIK
          PLQ.HVR.WDSVT..STLQI.G.GTFE.GVGCLDFSKADSGVHLCVIDDSNE.MLTVWDWQKKAKGAEIK
Retrocopy PLQRHVRAWDSVT<SSTLQINGVGTFEHGVGCLDFSKADSGVHLCVIDDSNEYMLTVWDWQKKAKGAEIK

Parental  TTNEVVLAVEFHPTDANTIITCGKSHIFFWTWSGN-SLTRKQGIFGKYEKPKFVQCLAFLGNGDVLTGDS
          TTNEVVLAVEFHPTD.NTIIT.GKS.IFFWTWSGN.SLTRKQGI.GKY.K.KFVQCLAFLGN.DVLTGDS
Retrocopy TTNEVVLAVEFHPTDGNTIITRGKSNIFFWTWSGN<SLTRKQGIWGKYGKQKFVQCLAFLGNRDVLTGDS

Parental  GGVMLIWSKT-TVEPTPGKGPKGIYQISKQIKA-HDGSVFTLCQMRNGMLLTGGGKDRKIILWDHDLN-S
          GGVML.W.KT...EP.PG.GPKG.YQ..KQIKA...G.VFTL.Q.RNGMLLTG.GKDRKIILWDHDLN.S
Retrocopy GGVMLLWNKT<SSEPIPGRGPKGVYQRGKQIKA<YNGRVFTLYQLRNGMLLTGRGKDRKIILWDHDLN<S

Parental  EREIEVPDQYG
          EREIEV.DQYG
Retrocopy EREIEVSDQYG

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	66.21 RPM
SRP051959_heart	0.00 RPM	20.70 RPM
SRP051959_kidney	0.04 RPM	51.52 RPM
SRP051959_liver	0.00 RPM	23.09 RPM
SRP051959_lung	0.03 RPM	65.07 RPM
SRP051959_lymph_node	0.00 RPM	113.31 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.92 RPM
SRP051959_spleen	0.02 RPM	77.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2217 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2217 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014719	1 retrocopy	retro_cjac_2217 ,