RetrogeneDB ID: retro_cjac_2813

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:61531592..61532730(-)
• Located in intron of: ENSCJAG00000015385

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_2813
ATAGCATCCACAGATTACAGTGCCTATAGCCAAGTTGCAGCACAGCAGGGCTACAGTGCTTACAACACACAGCCCACTCA
AGGATATACACAGACCACCTACGCATATGGTCAACAAAACTATGTAACCTATGGACAGCCCATTAATGTCAGCTACACCC
AGGCACAAACCACTGCAACCCATGGGCAGACTGCCTATGCAACTTCTTATGGACATCCTCCCACTGGTTATACTACTCCA
ACGTCCCCCAGGCATACAGCCAGCTTGTCCAGGGGTATGGCACTGGTGCTGATGATACCACCACTGCTACAGTCACCACC
ACCCAGGCCTCCTATGTAGCTCAGTCTGCATATGGCACTCAGCCTGCTTATCCAGCCTATGGGCAGCGGCTAGCAGCCAC
TGCACCTACAAGACTGCAGGATGGTAACAAGTCCACTGAGACTAGTCAACCTCAATGTAGCACAGGAGGTTTCAACCAGC
CCAGCCAAGGATATGGACAGAGTAACTACAGTTATCCCCAGGTTCCTGGGAGCTGCCCCATGCAGCCAGTCACTGCACCT
CCATCCTACCCTCTTACCAGCTATTCCTCTACACAGCCGACTAATTATGATCAGAGCAGTTACTCTCAGCAGAACACCTA
TGGGCAACTGAGCAGCTATAAATAGCAGAGTACCTATGGTCAACAAAGCAGCTATGGGCAGCAGCCTCCCACTAGTTATC
CACCCTAAACTGGACCCTACAGCTAGGCTCCAAATCAACATAGCCAACAGGGCAGCAGCTAAGGGCGCAGAGTTCATTCT
GACAGGACCACCCCAGTAGCATGGGTGTTTATGGGCAGGAGTCTGGAGGATTTTCTGAACCAGGAGGGAAATGGAGCATG
AGTGGCCCTGATAACTGGGGCAGGAGAAGAGGGGAATTTGATAGTGGGGTTGTGAGCAGATGTGGGCAAGGAGGAGGACA
TGGTGGAATGGGTGCTGGAGAGCAAGGTGGCTTCAAGAAGCCTGGTGGACCCATGGACAAAGGACCAGATCTTGATCTAG
ACCCACCTGTAGAAACTGATGAAGACTCTGACAACAGTGCAATCTATTTACAAGGATTAAATGATAATGTGACTCTAGAT
GATGTGGTAGACTTCTTC

Alignment

ORF - retro_cjac_2813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.03 %
• Parental protein coverage: 58.08 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASTDYSTYSQAAAQQGYSAYTAQPTQGYAQTTQAYGQQSYGTYGQPTDVSYTQAQTTATYGQTAYATSY
          .ASTDYS.YSQ.AAQQGYSAY..QPTQGY.QTT.AYGQQ.Y.TYGQP..VSYTQAQTTAT.GQTAYATSY
Retrocopy IASTDYSAYSQVAAQQGYSAYNTQPTQGYTQTTYAYGQQNYVTYGQPINVSYTQAQTTATHGQTAYATSY

Parental  GQPPTGYTTPTAP-QAYSQPVQGYGTGAYDTTTATVTTTQASYAAQSAYGTQPAYPAYGQQPAATAPTRP
          G.PPTGYTTPT.P.QAYSQ.VQGYGTGA.DTTTATVTTTQASY.AQSAYGTQPAYPAYGQ..AATAPTR.
Retrocopy GHPPTGYTTPTSP<QAYSQLVQGYGTGADDTTTATVTTTQASYVAQSAYGTQPAYPAYGQRLAATAPTRL

Parental  QDGNKPTETSQPQSSTGGYNQPSLGYGQSNYSYPQVPGSYPMQPVTAPPSYPPTSYSSTQPTSYDQSSYS
          QDGNK.TETSQPQ.STGG.NQPS.GYGQSNYSYPQVPGS.PMQPVTAPPSYP.TSYSSTQPT.YDQSSYS
Retrocopy QDGNKSTETSQPQCSTGGFNQPSQGYGQSNYSYPQVPGSCPMQPVTAPPSYPLTSYSSTQPTNYDQSSYS

Parental  QQNTYGQPSSYGQQSSYGQQSSYGQQPPTSYPPQTGSYSQAPSQYSQQSSSYGQ-QSSFRQDHPSSMGVY
          QQNTYGQ.SSY..QS.YGQQSSYGQQPPTSYPP.TG.YS.AP.Q.SQQ.SS.G..QSSF.QDHPSSMGVY
Retrocopy QQNTYGQLSSYK*QSTYGQQSSYGQQPPTSYPP*TGPYS*APNQHSQQGSS*GR<QSSF*QDHPSSMGVY

Parental  GQESGGFSGPGENRSMSGPDNRGRGRGGFDRGGMSRGGRGGGRGGMGSAGERGGFNKPGGPMDEGPDLDL
          GQESGGFS.PG...SMSGPDN.GR.RG.FD.G..SR.G.GGG.GGMG.AGE.GGF.KPGGPMD.GPDLDL
Retrocopy GQESGGFSEPGGKWSMSGPDNWGRRRGEFDSGVVSRCGQGGGHGGMG-AGEQGGFKKPGGPMDKGPDLDL

Parental  GPPVDPDEDSDNSAIYVQGLNDNVTLDDLADFF
          .PPV..DEDSDNSAIY.QGLNDNVTLDD..DFF
Retrocopy DPPVETDEDSDNSAIYLQGLNDNVTLDDVVDFF

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	0.27 RPM	44.73 RPM
SRP051959_heart	0.19 RPM	47.04 RPM
SRP051959_kidney	0.47 RPM	57.09 RPM
SRP051959_liver	0.41 RPM	43.10 RPM
SRP051959_lung	0.54 RPM	71.76 RPM
SRP051959_lymph_node	0.66 RPM	69.72 RPM
SRP051959_skeletal_muscle	0.07 RPM	41.91 RPM
SRP051959_spleen	0.36 RPM	60.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2813 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2813 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2813 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,