RetrogeneDB ID: retro_cjac_1416

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:76927548..76928615(-)
• Located in intron of: ENSCJAG00000008783

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011903
• Aliases: None
• Description: None

Sequence

>retro_cjac_1416
GCCATGCCGGCGGTATCAGCAAGTGCTCCTCCTGCCACACCAGCTCTGGCCCCAGCGGCGACCCCACAGTCTCGGCCCCA
ACCTCAGCACCAGCTGTGGCTCCGTCTTCCTCTGAGACTCCAGCCTCAACCTCAGACCCTGCGGCAGCAGCGGCTACGAC
TGCGGCTCCTGGCCAGACCGCGGCCTCAGCGCAAGCTCCCGCGCAGACCCCAGTGCTCGCTCTGCCTGGTCCCGCTCTCC
TAGGGCCCTTCCCCGGCAGCCGCGTGGTCAGGCTGCACCCAGTCATTTTGGCCTCCTTTATGGACAGCTACGAGCCACGC
AACCAGGGTGCTGCCCGAGTTATCAGAACCCTACTGGGAACGGTCGACAAGAACTCAGTGGAGGTCACCTGAAATTGCTT
TTCAGTGCCGCACAATGAGTCAGAAGATGAAGTGGCTGTTGACATGGAATTTGCTAAGAACGTGTATGAACTGCATAAAA
AAGTTTCTCCAAATGAGCTCATCCTGGGCTGGTACACTACAAGCCATGACATCACAGAGCACTCTGTGCTGATCCATGAG
TAATACAGCCGGGAGGCCCCAACCCCATCCACCTCACTGTGGACACAAGTCTCCAGAACGGCCACATTAGCATCGAAGCC
TATGTCAGCACTTTAATGGGTGTCCCTGGGAGGACCATGGAAGTGATGTTCACACCTCTGACAGTGAAATACGCATACTA
TGACAATGAACGAATTGGGAGTTGACCTGATCATGAAGACCTGCTTTAGCCCCAACCAAGTGACTGGACTCTCAAGTGAC
TTGCAGCAAGTAGGAGGGGCATCAGCTCGCATCCAGGATGCCCTGAGCACGGTGTTGCAATACACAGAGGATGTACTGTC
TGGAAAGGTGTCAGCTGACAATACTGTGGGCTGATTCCTGATGAAGCTGGTTAACCAAGTACCTAAAATAGTTCCTGATG
ACTTTGAGACCATGCTCAACAGCAACGTCAGTGACCTGCTGATGGTGACCTACCTGGCCAACGTCACACAGTCACAGATT
GCCCTCAATGAGAAACTTGTAAACCTG

Alignment

ORF - retro_cjac_1416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.96 %
• Parental protein coverage: 93.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  APPATPAPAPVAAPV-SAPTSVPA-PAPTPAQAAAPPSAGTPASSSDSAAAAATTAAPGQTSASAQAPAQ
          A.PA..A.AP.A.P..S.P...P...APT.A.A.AP.S..TPAS.SD.AAAAATTAAPGQT.ASAQAPAQ
Retrocopy AMPAVSASAPPATPA<SGPSGDPTVSAPTSAPAVAPSSSETPASTSDPAAAAATTAAPGQTAASAQAPAQ

Parental  TPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVT-NCFSVPHN
          TP..ALPGPAL.GPFPG.RVVRLHPVILAS..DSYE.RN.GAARVI.TLLGTVDK.SVEVT.NCFSVPHN
Retrocopy TPVLALPGPALLGPFPGSRVVRLHPVILASFMDSYEPRNQGAARVIRTLLGTVDKNSVEVT*NCFSVPHN

Parental  ESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAP-NPIHLTVDTSLQNG
          ESEDEVAVDMEFAKN.YELHKKVSPNELILGWY.T.HDITEHSVLIHE.YSREAP.NPIHLTVDTSLQNG
Retrocopy ESEDEVAVDMEFAKNVYELHKKVSPNELILGWYTTSHDITEHSVLIHE*YSREAP<NPIHLTVDTSLQNG

Parental  RMSIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIG-VDLIMKTCFSPNRVIGLSSDLQQVGGASAR
          ..SI.AYVSTLMGVPGRTM.VMFTPLTVKYAYYD.ERIG.VDLIMKTCFSPN.V.GLSSDLQQVGGASAR
Retrocopy HISIEAYVSTLMGVPGRTMEVMFTPLTVKYAYYDNERIG>VDLIMKTCFSPNQVTGLSSDLQQVGGASAR

Parental  IQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLANLTQSQI
          IQDALSTVLQY.EDVLSGKVSADNTVG.FLM.LVNQVPKIVPDDFETMLNSN..DLLMVTYLAN.TQSQI
Retrocopy IQDALSTVLQYTEDVLSGKVSADNTVG*FLMKLVNQVPKIVPDDFETMLNSNVSDLLMVTYLANVTQSQI

Parental  ALNEKLVNL
          ALNEKLVNL
Retrocopy ALNEKLVNL

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	1.22 RPM	24.25 RPM
SRP051959_heart	0.56 RPM	23.05 RPM
SRP051959_kidney	0.80 RPM	23.72 RPM
SRP051959_liver	0.50 RPM	20.36 RPM
SRP051959_lung	1.17 RPM	23.75 RPM
SRP051959_lymph_node	1.03 RPM	32.30 RPM
SRP051959_skeletal_muscle	0.66 RPM	31.21 RPM
SRP051959_spleen	0.67 RPM	29.14 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1416 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1416 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1416 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004861	1 retrocopy	retro_btau_527,
Canis familiaris	ENSCAFG00000006884	1 retrocopy	retro_cfam_1339,
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416 ,
Callithrix jacchus	ENSCJAG00000015129	2 retrocopies	retro_cjac_1520, retro_cjac_2910,
Erinaceus europaeus	ENSEEUG00000001226	1 retrocopy	retro_eeur_130,
Echinops telfairi	ENSETEG00000002717	2 retrocopies	retro_etel_1583, retro_etel_35,
Homo sapiens	ENSG00000175390	3 retrocopies	retro_hsap_2106, retro_hsap_2512, retro_hsap_4321,
Gorilla gorilla	ENSGGOG00000011702	5 retrocopies	retro_ggor_1566, retro_ggor_1567, retro_ggor_1568, retro_ggor_1589, retro_ggor_1590,
Myotis lucifugus	ENSMLUG00000000825	1 retrocopy	retro_mluc_2356,
Macaca mulatta	ENSMMUG00000015010	1 retrocopy	retro_mmul_412,
Oryctolagus cuniculus	ENSOCUG00000004225	1 retrocopy	retro_ocun_1488,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863,
Pongo abelii	ENSPPYG00000003512	1 retrocopy	retro_pabe_175,
Pan troglodytes	ENSPTRG00000003326	1 retrocopy	retro_ptro_197,
Pteropus vampyrus	ENSPVAG00000015764	1 retrocopy	retro_pvam_371,