RetrogeneDB ID: retro_cjac_1168

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:84665891..84667220(-)
• Located in intron of: ENSCJAG00000008117

Retrocopy information

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

Parental gene information

• Parental gene symbol: GDI2
• Ensembl ID: ENSCJAG00000020512
• Aliases: None
• Description: None

Sequence

>retro_cjac_1168
ATAAATGAGGACTACGATGTGATCGTGCTGGGCATCAGTCTGATGGAATGTATCTTTATTAGGTATAATGTCAGTGAATA
GCAAAAAAGTTCTTTATATGGATTGAAACTGTGGAGGAGAGAGTGCATCTATAATATCACTGGAAGATTTATACAAAAGA
TTTAAAATACCAGGATCACCACCAGAGTCAGTGGAGAGAGGAAGAGACTGTAGTGTTGATCTGATTCCCAAATTCCTTAT
GGCTAATGGTCAGCTGGTTAGGATGCTGCTTTATGCAGAGGTAACTCACTATCTGGATTTTAAAGTGACTGAAGGGAGCT
TTGTTTATGAGCATGGAAAAATATACAAAGTTCTTTCCACTAAAGCAGAAGCCCTGGTGTCTAGCTTAGTGGGACTGTTT
GAAAAATGTCACTTCAGGAAATTCCAAGTTTATGCTGCCAACTTCGATGAAAAAGATCTGAGAACTTTTGAAGGCATTGA
TCCTAAGAATACCACAATGCGAGAGGTGTATAAGAAATTTGATTTAGGTAAAGATGTTATAGATCTTTCTGGTTATGCTC
TTGCACTTTACAGAACTGATGACTACTTAGACCAACCATGTTGTGAAACCATTAATAGAATTAAACTTTACAGTGAGTCT
TTGTGAAGATATGGCAAAAGTCCATACCTTTATCTACTCTATGGCCTTGGAGAACTGCCCCAAGGATTTATAAGGCAAAG
TGCTGTTTATGGAGGTACCTATATGCTGACTAAACCCATTGGAGAAATCATTGTGCAGAATGGAAAAGTAATTGGTGTAA
TCTCTGAAGCAGAAATTGCTTGCAATAGGTAGCTCATCTGTGACCCCAGCTGTGTAAAAGATCAGGTAGAAAGGTGAGCC
AGGTGATCAGAGTTATTTTCATCCTCAGCCACCCCATCAAGAACACCAATGATGCCAACTCCTGCCAGATCATTATTCTA
CAGAACCAAGTTAATTGAAAATCGGGTATCTATGTCTGCATGGTCTCCTCTGAGCACAATGTAGCGGCACAAGGAAAGTA
CATTGCTGTAGTTAATACAACTGTGGAAACCAAGGAGCTAGAGGAGGAAATCAGACCAGCTTTGGCACTCTTGGAACCGA
TTGAACAGAAATTTGTTAGCATCAGTGACCTCCTGGTACCGAAAGACTTAGGAACAGAAAGCCAGATCTTTATTTCCCAC
ACATATGATGCTACCACTCATTTTGAGACAAAGTGTGATGACATTAAAAACATCTGTAAGAGGATGACAGGATCAGAGTT
GGACTTTGAGGAAATGAAACGCAAGAACAGTGACATCAATGGGGAAGAT

Alignment

ORF - retro_cjac_1168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.22 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNEEYDVIVLGTGLTECI-LSGIMSVNGKKVLHMDQNPYYGGESASITPLEDLYKRFKIPGSPPESMGRG
          .NE.YDVIVLG..L.ECI.L.GIMSVN.KKVL.MD.N...GGESASI..LEDLYKRFKIPGSPPES..RG
Retrocopy INEDYDVIVLGISLMECI>LLGIMSVNSKKVLYMD*N--CGGESASIISLEDLYKRFKIPGSPPESVERG

Parental  RDWNVDLIPKFLMANGQLVKMLLYTEVTRYLDFKVTEGSFVYKGGKIYKVPSTEAEALASSLMGLFEKRR
          RD..VDLIPKFLMANGQLV.MLLY.EVT.YLDFKVTEGSFVY..GKIYKV.ST.AEAL.SSL.GLFEK..
Retrocopy RDCSVDLIPKFLMANGQLVRMLLYAEVTHYLDFKVTEGSFVYEHGKIYKVLSTKAEALVSSLVGLFEKCH

Parental  FRKFLVYVANFDEKDPRTFEGIDPMKTTMREVYKKFDLGQDVIDFTGHALALYRTDDYLDQPCCETINRI
          FRKF.VY.ANFDEKD.RTFEGIDP..TTMREVYKKFDLG.DVID..G.ALALYRTDDYLDQPCCETINRI
Retrocopy FRKFQVYAANFDEKDLRTFEGIDPKNTTMREVYKKFDLGKDVIDLSGYALALYRTDDYLDQPCCETINRI

Parental  KLYSESLARYGKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPIEEIIVQNGKVIGVKSEGEIARCKQ
          KLYSESL.RYGKSPYLY.LYGLGELPQGF.R.SA.YGGTYML.KPI.EIIVQNGKVIGV.SE.EIA....
Retrocopy KLYSESL*RYGKSPYLYLLYGLGELPQGFIRQSAVYGGTYMLTKPIGEIIVQNGKVIGVISEAEIACNR*

Parental  LICDPSYVKDRVE-KVGQVIRVICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISSAHNVAAQGK
          LICDPS.VKD.VE.KV.QVIRVI.ILSHPIKNTNDANSCQIII.QNQVN.KS.IYVCM.SS.HNVAAQGK
Retrocopy LICDPSCVKDQVE<KVSQVIRVIFILSHPIKNTNDANSCQIIILQNQVN*KSGIYVCMVSSEHNVAAQGK

Parental  YIAIVSTTVETKEPEKEIRPALELLEPIEQKFISISDLLVPKDLGTESQIFISRTYDATTHFETTCDDIK
          YIA.V.TTVETKE.E.EIRPAL.LLEPIEQKF.SISDLLVPKDLGTESQIFIS.TYDATTHFET.CDDIK
Retrocopy YIAVVNTTVETKELEEEIRPALALLEPIEQKFVSISDLLVPKDLGTESQIFISHTYDATTHFETKCDDIK

Parental  NIYKRMTGSEFDFEEMKRKKNDIYGED
          NI.KRMTGSE.DFEEMKRK..DI.GED
Retrocopy NICKRMTGSELDFEEMKRKNSDINGED

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	1.69 RPM	95.32 RPM
SRP051959_heart	2.33 RPM	57.76 RPM
SRP051959_kidney	2.15 RPM	82.95 RPM
SRP051959_liver	0.69 RPM	111.51 RPM
SRP051959_lung	1.77 RPM	71.69 RPM
SRP051959_lymph_node	1.74 RPM	84.91 RPM
SRP051959_skeletal_muscle	2.27 RPM	36.51 RPM
SRP051959_spleen	1.83 RPM	105.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1168 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1168 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
Bos taurus	ENSBTAG00000005316	1 retrocopy	retro_btau_1208,
Canis familiaris	ENSCAFG00000005223	2 retrocopies	retro_cfam_2196, retro_cfam_886,
Callithrix jacchus	ENSCJAG00000020512	2 retrocopies	retro_cjac_1168 , retro_cjac_3115,
Cavia porcellus	ENSCPOG00000013449	1 retrocopy	retro_cpor_696,
Gorilla gorilla	ENSGGOG00000003623	1 retrocopy	retro_ggor_2590,
Mus musculus	ENSMUSG00000021218	2 retrocopies	retro_mmus_2971, retro_mmus_360,
Oryctolagus cuniculus	ENSOCUG00000005367	1 retrocopy	retro_ocun_69,
Ictidomys tridecemlineatus	ENSSTOG00000006449	1 retrocopy	retro_itri_757,
Tupaia belangeri	ENSTBEG00000011523	1 retrocopy	retro_tbel_644,