RetrogeneDB ID: retro_cjac_2911

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:87084911..87086060(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021737
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019987
• Aliases: None
• Description: None

Sequence

>retro_cjac_2911
CAGCCTCCCACTAGTTACCCACCCCAAACTGGATCCTACTGCCAGGATCCAAGTCAATATAGCCAACAGAGCAGCAGCTA
CGGGCAGCAGAGTTCATTCCAACAGGACCACCCCAGTAGCATGGGTGTTTATGGGCAGGAGTCAGGAGGATTTTCCAGAC
CAGGAGAGAACCAGAGCATGAGTGGTCCTGATAACTGGGGCAGGGGAAGGGGGGGATTTGATCGTGGAGGCATGAGCAGA
GGTGGGCAGGGAGGAGGACGCAGTGGAATCGGCAGCGCTGGAGAGTGAGGTGGCTTCAATAAGCCTGGTGGACCCATGGA
CGAAGGAGCAGATCTTGATCTAGGCCCACCTGTAGATCCAGATGAAGACTCTGACAACAATGCAATTTATGTACAAGGAT
TAAATGATAATGTGACTCTAGATGATCTGGCAGACTTCTTTAAGCAGTGTGGGGTTGTTAAGATGAACAAGAGAACTGGG
CAACCCATGATCCGCATCTACCTGGACAAGGAAACAGGAAAGTCCAAAGGCGATGCCACAGTATCCTATGAAGACCCACC
TACTGCCAAGGCTGCTGTGGAGTGGTTTGACAGTAAAGATTTTCAAGGGAGCAAACTTAAAGTCTCTCTTGCTCAGAAGA
AGCCTCCAGTGAACAGTATGAGGGGTGGTATGCCACCCCGTGAGGGCAGAGGGATGTCACCACCACTCTGTGGAGGTCTA
GAAGGCCCAGGATGTCCTGGGGGACCCATGGGTTGCATGGGAGGCCATGGAGGAGATAGAGGAGGCTTCCCTCCCAGAGG
ACCCTGGGGTTCCCAAGGGAACCCCTCCAGAGGAAGAAACGTCCAGCACCAAGCTGGAGACTGGCAGTGTCCCAGTCCAG
GTTGTTGAAACCAGAACTTCGCCTGAAGAACAGAGTGCAACCAGTGTAAAGCCCCAAAGCCTGAAGCCTTCCTCCCGCCA
CCATTCCCGCCCCTGGATGGTGATCATGTCAGAGGAGGCCCTGGTGGCATGCGGGGAGGAAGAAGTGGACTCATGGATTG
TGGTGGTCCCGGTGGAATGTTCAGAGGTGGCCGTGGTGGAGACAGAGGTGGTTTCCGTGATGGCCGGGGCGTGAACTGAA
GTGGCTTTGGTGGAGGAAGATGAAATGGG

Alignment

ORF - retro_cjac_2911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.73 %
• Parental protein coverage: 57.79 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QPPTSYPPQTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGR
          QPPTSYPPQTGSY.Q.PSQYSQQSSSYGQQSSF.QDHPSSMGVYGQESGGFS.PGEN.SMSGPDN.GRGR
Retrocopy QPPTSYPPQTGSYCQDPSQYSQQSSSYGQQSSFQQDHPSSMGVYGQESGGFSRPGENQSMSGPDNWGRGR

Parental  GGFDRGGMSRGGRGGGRGGMG-AGERGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIYVQGLNDNVTL
          GGFDRGGMSRGG.GGGR.G.G.AGE.GGFNKPGGPMDEG.DLDLGPPVDPDEDSDN.AIYVQGLNDNVTL
Retrocopy GGFDRGGMSRGGQGGGRSGIGSAGE*GGFNKPGGPMDEGADLDLGPPVDPDEDSDNNAIYVQGLNDNVTL

Parental  DDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSL
          DDLADFFKQCGVVKMNKRTGQPMI.IYLDKETGK.KGDATVSYEDPPTAKAAVEWFD.KDFQGSKLKVSL
Retrocopy DDLADFFKQCGVVKMNKRTGQPMIRIYLDKETGKSKGDATVSYEDPPTAKAAVEWFDSKDFQGSKLKVSL

Parental  ARKKPPMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGGN
          A.KKPP.NSMRGGMPPREGRGM.PPL.GG..GPG.PGGPMG.MGG.GGDRGGFPPRGP.GS.GNPS.G.N
Retrocopy AQKKPPVNSMRGGMPPREGRGMSPPLCGGLEGPGCPGGPMGCMGGHGGDRGGFPPRGPWGSQGNPSRGRN

Parental  VQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGGDRGRGGPGGMRGGRGGLMDRGGP
          VQH.AGDWQCP.PGC.NQNFA.RTECNQCKAPKPE.FLPPPFPP..GD..RGGPGGMRGGR.GLMD.GGP
Retrocopy VQHQAGDWQCPSPGC*NQNFA*RTECNQCKAPKPEAFLPPPFPPLDGDHVRGGPGGMRGGRSGLMDCGGP

Parental  GGMFRGGRGGDRGGFRGGRGMDRGGFGGGRRGG
          GGMFRGGRGGDRGGFR.GRG....GFGGGR..G
Retrocopy GGMFRGGRGGDRGGFRDGRGVN*SGFGGGR*NG

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	0.02 RPM	44.73 RPM
SRP051959_heart	0.04 RPM	47.04 RPM
SRP051959_kidney	0.04 RPM	57.09 RPM
SRP051959_liver	0.04 RPM	43.10 RPM
SRP051959_lung	0.07 RPM	71.76 RPM
SRP051959_lymph_node	0.05 RPM	69.72 RPM
SRP051959_skeletal_muscle	0.04 RPM	41.91 RPM
SRP051959_spleen	0.02 RPM	60.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2911 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2911 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2911 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008298	2 retrocopies	retro_amel_191, retro_amel_959,
Canis familiaris	ENSCAFG00000012160	8 retrocopies	retro_cfam_1142, retro_cfam_1183, retro_cfam_1225, retro_cfam_133, retro_cfam_1397, retro_cfam_1736, retro_cfam_1889, retro_cfam_560,
Callithrix jacchus	ENSCJAG00000019987	4 retrocopies	retro_cjac_1716, retro_cjac_2022, retro_cjac_2813, retro_cjac_2911 ,
Cavia porcellus	ENSCPOG00000009502	1 retrocopy	retro_cpor_1353,
Felis catus	ENSFCAG00000004243	1 retrocopy	retro_fcat_519,
Homo sapiens	ENSG00000182944	1 retrocopy	retro_hsap_463,
Gorilla gorilla	ENSGGOG00000012212	1 retrocopy	retro_ggor_444,
Macropus eugenii	ENSMEUG00000008703	1 retrocopy	retro_meug_1424,
Myotis lucifugus	ENSMLUG00000012058	1 retrocopy	retro_mluc_328,
Monodelphis domestica	ENSMODG00000008679	1 retrocopy	retro_mdom_279,
Mustela putorius furo	ENSMPUG00000013432	2 retrocopies	retro_mputfur_56, retro_mputfur_572,
Mus musculus	ENSMUSG00000009079	1 retrocopy	retro_mmus_1379,
Oryctolagus cuniculus	ENSOCUG00000004432	2 retrocopies	retro_ocun_1346, retro_ocun_242,
Pongo abelii	ENSPPYG00000011684	1 retrocopy	retro_pabe_1769,
Pan troglodytes	ENSPTRG00000014218	1 retrocopy	retro_ptro_350,
Ictidomys tridecemlineatus	ENSSTOG00000023177	1 retrocopy	retro_itri_1892,
Tursiops truncatus	ENSTTRG00000011881	1 retrocopy	retro_ttru_1366,