RetrogeneDB ID: retro_cjac_1716

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:47287416..47288712(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cjac_1716
ACCAGCTATTCCTCTACACAGCCGACTAGTTATGATGAAAGCAGTTACTCTCAGCAGAACACCCATGGGCAACCGAGCAG
CTATGGACAGCAGAGTAGCTAGAGCAGCAGCTACGGGCAGCAGAGTTCATTCCGACAGGACCACCCCAGTAGCACGGGTG
TTTATGGGCAGGAGTCTGGAGGATTTTCCGGACCAGGAGAGAACCGGAGCATGAGTGGCCCTGATAACCGGGGCAGGGGA
AGAGGGGGATTTGATCGTGGAGGCATGAGCAGAGGTGGGCAGGGAGGAGGACACGGTGGAATGGGCGCTGGAGAGCGAGG
TGGCTTCAATAAGCCTGGTGGACCCATGGACGAGGGGCCAGATCTTGATCTAGGCCCACCTGTAGATCCAGATGAAGATT
CTGACAACAGTGCAATTTATGTACAAGGATTAAATGATAATGTGACTCTAGATGATCTGGCAGACTTCTTTAAGCAGTGT
GGGGTTGTTAAGATGAACAAGAGAACTGGGCAACCCATGATCCACATCTACCTGGACAAGGAAACAGGAAAGCCCAAAGG
CGATGCCACAGTATCCTATGAAGACCCACCTACTGCCAAGGCTGCCGTGGAGTGGTTTGACGGTAAAGACTTTCAAGGGA
GCAAACTTAAAGTCTCTCTTGCTCGGAAGAAGCCTCCAATGAACAGTATGCGAGGCGGTATGCCACCCCGTGAGGGCAGA
GGGATGCCACCACCACTCCGTGGAGGTCCAGGAGGCCCAGGAGGTCCTGGGGGACCCATGGGTCGCATGGGAGGCCATGG
AGGAGATAGAGGAGGCTTCCCTCCCAGAGGACCCCGGGGTTCCCGAGGGAACCCCTCCGGCGGAGGAAACGTCCAGCACA
GAGCTGGAGACTGGCAGTGTCCCAATCCGGGTTGTGGAAACCAGAACTTCGCCTGGAGAACAGAGTGCAACCAGTGTAAG
GCCCCAAAGCCTGAAGGCTTCCTCCCGCCACCCTTCCCGCCCCTGGGTGGTGATCGTGGCAGAGGTGGCCCTGGTGGCAT
GCGGGGAGGAAGAGGTGGCCTCATGGATCGTGGTGGTCCCGGTGGAATGTTCAGAGGTGGCCGTGGAGGAGACAGAGGTG
GCTTCCGTGGTGGCCGGGGCATGGACCGAGGTGGCTTTGGTGGAGGAAGACGAGGTGGCCCTGGGGGGCCCCCTGGACCT
TTGATGGAACAGATGGGAGGAAGAAGAGGAGGACGTGGAGGACCTGGAAAAATGGATAAAGGCGAGCACCATCAGGAGTG
CAGAGATCGGCCCTAT

Alignment

ORF - retro_cjac_1716 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.29 %
• Parental protein coverage: 64.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSYGQQPPTSYPPQTGSYSQA---PSQYSQQ---SSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENRS
          .SY....PTSY.....S.......PS.Y.QQ...SSSYGQQSSFRQDHPSS.GVYGQESGGFSGPGENRS
Retrocopy TSYSSTQPTSYDESSYSQQNTHGQPSSYGQQSS*SSSYGQQSSFRQDHPSSTGVYGQESGGFSGPGENRS

Parental  MSGPDNRGRGRGGFDRGGMSRGGRGGGRGGMGAGERGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIY
          MSGPDNRGRGRGGFDRGGMSRGG.GGG.GGMGAGERGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIY
Retrocopy MSGPDNRGRGRGGFDRGGMSRGGQGGGHGGMGAGERGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIY

Parental  VQGLNDNVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD
          VQGLNDNVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD
Retrocopy VQGLNDNVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD

Parental  FQGSKLKVSLARKKPPMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRG
          FQGSKLKVSLARKKPPMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGG.GGDRGGFPPRGPRG
Retrocopy FQGSKLKVSLARKKPPMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGHGGDRGGFPPRGPRG

Parental  SRGNPSGGGNVQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGGDRGRGGPGGMRGG
          SRGNPSGGGNVQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPP.GGDRGRGGPGGMRGG
Retrocopy SRGNPSGGGNVQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPLGGDRGRGGPGGMRGG

Parental  RGGLMDRGGPGGMFRGGRGGDRGGFRGGRGMDRGGFGGGRRGGPGGPPGPLMEQMGGRRGGRGGPGKMDK
          RGGLMDRGGPGGMFRGGRGGDRGGFRGGRGMDRGGFGGGRRGGPGGPPGPLMEQMGGRRGGRGGPGKMDK
Retrocopy RGGLMDRGGPGGMFRGGRGGDRGGFRGGRGMDRGGFGGGRRGGPGGPPGPLMEQMGGRRGGRGGPGKMDK

Parental  GEHRQERRDRPY
          GEH.QE.RDRPY
Retrocopy GEHHQECRDRPY

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	0.11 RPM	44.73 RPM
SRP051959_heart	0.11 RPM	47.04 RPM
SRP051959_kidney	0.13 RPM	57.09 RPM
SRP051959_liver	0.13 RPM	43.10 RPM
SRP051959_lung	0.16 RPM	71.76 RPM
SRP051959_lymph_node	0.05 RPM	69.72 RPM
SRP051959_skeletal_muscle	0.07 RPM	41.91 RPM
SRP051959_spleen	0.11 RPM	60.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1716 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1716 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1716 has 0 orthologous retrocopies within eutheria group .

---

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,