RetrogeneDB ID: retro_cjac_213

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:123732307..123734065(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022490
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FZD8
• Ensembl ID: ENSCJAG00000014119
• Aliases: None
• Description: None

Sequence

>retro_cjac_213
ATGGCTCGGCCTGACCCGTCCGCGCCGCCGTCTCTGCTGCTGCTGCTCCTGGCGCAGCTGGCGGGCCGGGCGACCGCCGC
ATCCAAGGCCCCGGTGTGCCAAGAAATCACGGTGCCCATGTGCCGCGGCATCGGCTACAACCTGACGCACATGCCCAACC
AGTTCAACCACGACACGCAGGACGAGGCGGGCCTGGAGGTGCACCAGTTCTGGCCGCTGGTGGAGATCCACTGTTCGCCG
GACCTGCGCTTCTTCCTGTGCTCCATGTACACGCCCATCTGCCTGCCCGACTATCACAAGCCGCTACCGCCCTGCCGCTC
GGTGTGCGAGCGCGCCAAGGCCGGCTGCTCGCCGCTCATGCGCCAGTACGGCTTCGCTTGGCCGGAGCGCATGAGCTGCG
ACCGCCTCCCGGTGCTGGGCCGCGACGCCGAGGTCCTGTGCATGGATTACAACCGCAGCGAGGCCACCACGGCTCCCCCC
AGGGCCTTCCCAGCCAAGCCCACACTTCCAGGCCCACCAGGGGCGCCGGCCTCAGGGGGCGAATGCCCCGCTGGGGGCCC
GTCTGTGTGCAAGTGTCGCGATCCCTTCGTGCCGATCCTGAAGGAGTCACACCCGCTCTACAACAAGGTGCGGACGGGGC
AGGTGCCCAACTGCGCGGTACCCTGCTACCAGCCGTCCTTCAGTTCCGATGAGCGCACGTTCGCCACCTTCTGGATCGGC
CTGTGGTCGGTGCTGTGCTTCATCTCCACGTCCACCACAGTGGCCACGTTCCTCATCGACATGGAACGCTTCCGCTATCC
TGAGCGCCCCATCATCTTCCTGTCCGCCTGTTACCTATGCGTGTCGCTGGGCTTCCTAGTTCGCCTGGTCGTGGGCCATG
CCAGCGTGGCCTGCAGCCGTGAGCACAACCACATCCACTACGAGACCACGGGCCCTGCGCTGTGCACCATTGTCTTCCTC
CTGGTCTACTTCTTCGGCATGGCCAGCTCCATCTGGTGGGTCATCCTGTCGCTCACCTGGTTCCTGGCAGCCGGCATGAA
GTGGGGCAATGAGGCCATCGCGGGCTACGCGCAGTACTTCCACCGGGCTGCGTGGCTCATCCCCAGCGTCAAATCCATCA
CGGCGCTGGCGCTGAGCTCCGTGGACGGGGACCCGGTGGCTGGCATCTGCTACGTGGGCAACCAGAACCTGAACTCGCTG
CGCGGCTTCGTGCTGGGCCCGCTGGTGCTCTACCTGTTGGTGGGCACGCTCTTCCTGCTGGCGGGCTTTGTGTCGCTCTT
CCGCATCCGTAGCGTCATCAAGCAGGGCGGCACCAAGACGGACAAGCTGGAGAAGCTCATGATCCGCATCGGCATCTTCA
CGCTGCTCTACACGGTGCCCGCCAGCATCGTGGTGGCCTGCTACCTGTACGAGCAGCACTATCGCGAGAGCTGGGAGGCG
GCGCTCACCTGTGCCTGCCCGGCCCCCGACGCCGGCCAGCCGCGCGCCAAGCCCGAGTACTGGGTGCTCATGCTCAAGTA
CTTCATGTGCCTGGTGGTGGGCATCACGTCGGGTGTCTGGATCTGGTCGGGCAAGACGGTGGAGTCGTGGCGGCGTTTCA
CCAGCCGCTGCTGCTGCCGCCCGCGGCGCGGCCACAAGAGCGGGGGCGCCATGGCCGCCGGGGACTACCCCGAGGCCAGC
GCGGCACTCACGGGCAGGACCGGGCCGCCGGGCCCCGCCGCCGCCTACCACAAACAGGTGTCCCTGTCGCACGTGTAG

Alignment

ORF - retro_cjac_213 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.89 %
• Parental protein coverage: 58.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CQCRAPMVSVSSERHPLYNRVKTGQIANCALPCHNPFFSQDERAFTVFWIGLWSVLCFVSTFPTVSTFLI
          C.CR.P.V....E.HPLYN.V.TGQ..NCA.PC..P.FS.DER.F..FWIGLWSVLCF.ST..TV.TFLI
Retrocopy CKCRDPFVPILKESHPLYNKVRTGQVPNCAVPCYQPSFSSDERTFATFWIGLWSVLCFISTSTTVATFLI

Parental  DMERFKYPERPIIFLSACYLFLSVGYLVRLVAGHEYEELGAVEHHVRYKTTGPALCSVVFLLVYFLVMAS
          DMERF.YPERPIIFLSACYL..S.G.LVRLV.GH..........H..Y.TTGPALC..VFLLVYF..MAS
Retrocopy DMERFRYPERPIIFLSACYLCVSLGFLVRLVVGHASVACSREHNHIHYETTGPALCTIVFLLVYFFGMAS

Parental  SIWWVILSLTWFLEAGMKWGNETIAGYSQYFHLATWLVPNI-SIAVLALNSVDGDPVAGICYLVNHSLYN
          SIWWVILSLTWFL.AGMKWGNE.IAGY.QYFH.A.WL.P...SI..LAL.SVDGDPVAGICY..N..L..
Retrocopy SIWWVILSLTWFLAAGMKWGNEAIAGYAQYFHRAAWLIPSVKSITALALSSVDGDPVAGICYVGNQNLNS

Parental  LRGLVLAPLVIYLFMYIKILLTIFALLLSIFFFFKHQVVPTIKHNRIK---GLKQVIYTNKKEEVVEYIF
          LRG.VL.PLV.YL......LL..F..L..I....K.....T.K........G.....YT.....VV....
Retrocopy LRGFVLGPLVLYLLVGTLFLLAGFVSLFRIRSVIKQGGTKTDKLEKLMIRIGIFTLLYTVPASIVVACYL

Parental  IEQHNRPRWEATHNCPCLRDLQPDQARRPDYAVFMLKYFMCLVVGITSGVWVWSGKTLESWRSLCTRCC
          .EQH.R..WEA...C.C...........P.Y.V.MLKYFMCLVVGITSGVW.WSGKT.ESWR....RCC
Retrocopy YEQHYRESWEAALTCACPAPDAGQPRAKPEYWVLMLKYFMCLVVGITSGVWIWSGKTVESWRRFTSRCC

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	8.92 RPM	0.62 RPM
SRP051959_heart	1.79 RPM	7.30 RPM
SRP051959_kidney	8.39 RPM	2.00 RPM
SRP051959_liver	3.36 RPM	0.65 RPM
SRP051959_lung	1.53 RPM	1.74 RPM
SRP051959_lymph_node	0.21 RPM	0.46 RPM
SRP051959_skeletal_muscle	1.51 RPM	0.57 RPM
SRP051959_spleen	0.15 RPM	3.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_213 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_213 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_213 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001137	1 retrocopy	retro_acar_5,
Callithrix jacchus	ENSCJAG00000014119	1 retrocopy	retro_cjac_213 ,
Ficedula albicollis	ENSFALG00000007019	1 retrocopy	retro_falb_7,
Petromyzon marinus	ENSPMAG00000005873	1 retrocopy	retro_pmar_8,