RetrogeneDB ID: retro_cjac_1970

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:155383275..155385182(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBC1D25
• Ensembl ID: ENSCJAG00000002300
• Aliases: None
• Description: None

Sequence

>retro_cjac_1970
AAGAAATGTGAGAGCTTCTTGGCGCCGGGTTCCGCTCTTTTGCTGTAGATCCCAGATCACCTCACTTAATGTGTTGAAGC
ACATTCTCTTCCGAGCCTTTGATTTGAGTGGGAAGAACTCTGGCATCAGCTACCTGGGCCGGGACCGGCTAGAACAGGAA
GCTTACCTCTCACTCCTATCTGACTGGGACCTCAGCACAGCCTTTGCTACTGCCTCCGAACCTTACCTGCAATTGCGCAT
AGATATTCGGCCCTCGGAGTACAGCCCATTGCTGGAAGACTGGGACATAATCAGTCCCAAAGATGTCATTGGCTGCGACG
TGTTGCTGGCTGAGAAACGATCATCACTGACGACTGCTGCCCTGCTCTTTACACAGTCCATCCTCACTCAGGTGGTCCGT
ACCTTGTCTAAGGTCCAACAAGTACTGAGCTGGTCGTATGGGGAAGATGTCAAGCCCTTCAAGCCACCCTTAAGCGATGC
TGAGTTTCACGCATACCTGAACCCCGAGGGCCGGCTCTCCTGACCTGAGGAGTTGCGCCTGCGGATCTGTCGTGGTGGTG
TGGAGCCCTCACTGCGAAAGGTGGTGTGGCGGTACCTGTTAAACGTGTATCCAGATGGACTGAAAGGCCGAGAGCGGATG
GACTACATGAAACGCAAGAGCCGCGAGTATGAGCAGCTCAAGAGCGAGTGGGCCCAGCGAGCAAGCCCTGAGGACCTGAA
ATTCATCCGCAGCACCGTCCTCAAGGATGTGCTGTGCACTGATCGGGCCCACCCCTACTATGCAGGGCCTGAGGATGGCC
CACATCTACGGGCGCTGCACAACCTGCTCACCACCTATGCCGTTACCCACCCACAGGTGTCCTGCCACGGCCTGAGTGAC
CTTGCCTTACCCATCCTCGCTGTCATGGACCACGAGGGCCATGCCTTTGTCTGCTTTTGTGGCATCATGAAGCGTCTGGC
CGCCAACTTCCACCTGACGGCCGGGCCATGGCTACCAAGTTTGCACACCTGAAGCTGTTGCTGCGACACGCCGACCCTGA
CTTTTACCAATACCTGCAAGAGGCAGGCACTGATGACCACTTCTTCTGTTACCGCTGGCTGCTGCTGGAGCTCAAGCGTG
AGTTCGCCTTTGACGACGCCCTCCGCATGCCTGAGGTCACCTGGAGTTCGCTGCCTCCTGATCCTCCTGAACATGAGGTA
AAGCTGGTTGGATCCCCCAGCCAAGCAGACACTGGCTTTGGTGGCCACAGGGGGTGGCCTCTGCGACAGAGGCACAGGCT
GAAGCCTGCCGTGGAGGAGGTAGAACCTTTGAAGATGCTGTTGACCACCTGGCCATAGCCGGCCAGGAGCCTAGTAGTGG
GGGACGTCTCCTGAGACAAGCCAGCTTGGATGGTCTCCAGCAACTCAGGGATAACATGGGCTCCAGGAGGGGCCCTCTGG
TCCAGCTGCCCCATCCGGCTGCCCTTATCAGCTCCAAGTCCCTCTACGAGCCTTTATTGAACTCCCCAGATCCACTGCTC
TCCTTCTTTTCCCACCCTGATTCCCCATCTTCCTCATCTCCACCATCTACCCAGGAGGCCTCTCCCACTGGTGAAATGGC
TGTAGGATCCCCCATGATGCAAGAGGTGGGCTCCCTGAAAGACCCAGGAAAGTCCCTGCCACCCGTACCACCAATGGGCC
TGCCCCAGCCCCAGGAGTTTGGCGGGGGAAACCCATTCATGCTGTTCCTCTGCCTGGCGATCCTGCTGGAACACCGCGAT
CACATCATGCTCAATGGGCTGGATTATAACGAGTTGGCCATGCACTTTGACCACTTAGTGCGAAAACACCACCTAGGGCG
CGTCCTGCGCCGGAGCCGGGCTCTCTTTGCTGATTACCGGCAGTCAGAGGTGTGGGACTCAGAGGAG

Alignment

ORF - retro_cjac_1970 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.14 %
• Parental protein coverage: 93.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KKCESFLAPE-FRSFAVDP-QITSLDVLQHILIRAFDLSGKKNFGISYLGRDRLGQEAYLSLLSDWDLST
          KKCESFLAP..FRSFAVDP.QITSL.VL.HIL.RAFDLSGK.N.GISYLGRDRL.QEAYLSLLSDWDLST
Retrocopy KKCESFLAPG<FRSFAVDP<QITSLNVLKHILFRAFDLSGK-NSGISYLGRDRLEQEAYLSLLSDWDLST

Parental  AFAAASKPYLQLRVDIRPSEDSPLLEDWDIISPKDVIGSDVLLAEKRSSLTTAALPFTQSILTQVGRTLS
          AFA.AS.PYLQLR.DIRPSE.SPLLEDWDIISPKDVIG.DVLLAEKRSSLTTAAL.FTQSILTQV.RTLS
Retrocopy AFATASEPYLQLRIDIRPSEYSPLLEDWDIISPKDVIGCDVLLAEKRSSLTTAALLFTQSILTQVVRTLS

Parental  KVQQVLSWSYGEDVKPFKPPLSDAEFHTYLNHEGQLSRPEELRLRIYHGGVEPSLRKVVWRYLLNVYPDG
          KVQQVLSWSYGEDVKPFKPPLSDAEFH.YLN.EG.LS.PEELRLRI..GGVEPSLRKVVWRYLLNVYPDG
Retrocopy KVQQVLSWSYGEDVKPFKPPLSDAEFHAYLNPEGRLS*PEELRLRICRGGVEPSLRKVVWRYLLNVYPDG

Parental  LTGRERMDYMKRKSREYEQLKSEWAQRASPEDLEFIRSTVLKDVLRTDRAHPYYAGPEDGPHLRALHDLL
          L.GRERMDYMKRKSREYEQLKSEWAQRASPEDL.FIRSTVLKDVL.TDRAHPYYAGPEDGPHLRALH.LL
Retrocopy LKGRERMDYMKRKSREYEQLKSEWAQRASPEDLKFIRSTVLKDVLCTDRAHPYYAGPEDGPHLRALHNLL

Parental  TTYAVTHPQVSYCQGMSDLASPILAVMDHEGHAFVCFCGIMKRLAANFH-PDGRAMATKFAHLKLLLRHA
          TTYAVTHPQVS.C.G.SDLA.PILAVMDHEGHAFVCFCGIMKRLAANFH.PDGRAMATKFAHLKLLLRHA
Retrocopy TTYAVTHPQVS-CHGLSDLALPILAVMDHEGHAFVCFCGIMKRLAANFH<PDGRAMATKFAHLKLLLRHA

Parental  DPDFYQYLQEAGADDLFFCYRWLLLELKREFAFDDALRMLEVTWSSLPPDPPEHEVELVGPPSQADTGFG
          DPDFYQYLQEAG.DD.FFCYRWLLLELKREFAFDDALRM.EVTWSSLPPDPPEHEV.LVG.PSQADTGFG
Retrocopy DPDFYQYLQEAGTDDHFFCYRWLLLELKREFAFDDALRMPEVTWSSLPPDPPEHEVKLVGSPSQADTGFG

Parental  GHRGWPVRQRHMLRPA-SGGGSTFEDAVDHLATASQGPGGGGRLLRQASLDGLQQLRDNMGSRRGPLVQL
          GHRGWP.RQRH.L.PA..GGG.TFEDAVDHLA.A.Q.P..GGRLLRQASLDGLQQLRDNMGSRRGPLVQL
Retrocopy GHRGWPLRQRHRLKPA<RGGGRTFEDAVDHLAIAGQEPSSGGRLLRQASLDGLQQLRDNMGSRRGPLVQL

Parental  PHPAALISSKSLSEPLLNSPDPLLSSFSHPDSPSSSSPPSTQEASPTGDMAVGSPMMQEVGSPKDPGKSL
          PHPAALISSKSL.EPLLNSPDPLLS.FSHPDSPSSSSPPSTQEASPTG.MAVGSPMMQEVGS.KDPGKSL
Retrocopy PHPAALISSKSLYEPLLNSPDPLLSFFSHPDSPSSSSPPSTQEASPTGEMAVGSPMMQEVGSLKDPGKSL

Parental  PPVPPMGLPPPQEFGRGNPFMLFLCLAILLEHRDHIMRNGLDYNELAMHFDRLVRKHHLGRVLRRARALF
          PPVPPMGLP.PQEFG.GNPFMLFLCLAILLEHRDHIM.NGLDYNELAMHFD.LVRKHHLGRVLRR.RALF
Retrocopy PPVPPMGLPQPQEFGGGNPFMLFLCLAILLEHRDHIMLNGLDYNELAMHFDHLVRKHHLGRVLRRSRALF

Parental  ADYLQSEVWDSEE
          ADY.QSEVWDSEE
Retrocopy ADYRQSEVWDSEE

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	3.00 RPM
SRP051959_heart	0.00 RPM	2.58 RPM
SRP051959_kidney	0.00 RPM	2.60 RPM
SRP051959_liver	0.00 RPM	1.19 RPM
SRP051959_lung	0.00 RPM	4.16 RPM
SRP051959_lymph_node	0.00 RPM	3.10 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.38 RPM
SRP051959_spleen	0.00 RPM	3.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1970 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1970 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1970 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002300	1 retrocopy	retro_cjac_1970 ,
Myotis lucifugus	ENSMLUG00000003989	1 retrocopy	retro_mluc_280,