RetrogeneDB ID: retro_cjac_720

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:94375259..94376110(+)
• Located in intron of: ENSCJAG00000015006

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011795
• Aliases: None
• Description: None

Sequence

>retro_cjac_720
ATGCCAGCAGCAACTGTAGATCATAGCCAAAGAATTTGTGAAGTTTGGGTTTGCAGCTTGAAGAGATGAAGAAAGCTCGT
CCAGTTATCCGAAAATATAATTACATTGCTGTGGACACCGAATTTCCAGGTGTGGTTGCAAGACCCACTGGAGAATTCAG
GAGCAATGCTGACTATCAATACCAACTACTGGGATGTAATGTAGACTTGTTAAGGATAATTCAGCTAGGACTGACATTTA
TGAATGAGCAAGGGGAATACCCTCCAAGAACTCCAACACGGCAGTTGAATTTCAAATTTAATTTGACGGAAGACATGTAT
GCCCAGGACTCTACAGAGCTACTAACAACATCTGATATCCAGTTTTAAAAACATGAGGAGGAAGGAATTGAGACCCAGTA
CTTCGCAGAACTTCTTATGACTTCAGGAGTGGTCCTCTGTGAAGGCGTCAAATGGTTGTCATTTCATAGCGGTTACGACT
TTGGCTATTTAATCAAAATCCTGACCAACTCTAACTTGCCTGAAGAAGAACTTGACTTCTTTAAGATCCTTCAATTGTTT
TTTTCCTGTCATTTATGATGTGAAGTACCTCATGAAGAGCTGCAAAAATCTCAAAGGTGGATTACAGAAGTGGCAGAACA
GTAAGAGCTGGAACGGATAGGACCACGACATCAGGCAGGATCTGATGCATTGCTCATAGGAATCGCCTTTTTCAAAATGA
GAGAAATGTTCTTTGAAGATCATATTGATGATGCCAAATATTATGGTCATTTGTACGGCCTTGGTTCTGGTTCATCCTAT
GTACAGAATGGCACAGGGAATGCATATGAAGAGGAAGTCAACAAGCAGTCA

Alignment

ORF - retro_cjac_720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPAATVDHSQRICEVWACN-LDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNV
          MPAATVDHSQRICEVW.C..L.E..K..R.VIRKYNY.A.DTEFPGVVARP.GEFRSNADYQYQLL.CNV
Retrocopy MPAATVDHSQRICEVWVCS<LEEMKK-ARPVIRKYNYIAVDTEFPGVVARPTGEFRSNADYQYQLLGCNV

Parental  DLLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAEL
          DLL.IIQLGLTFMNEQGEYPP.T.T.Q.NFKFNLTEDMYAQDS.ELLTTS.IQF.KHEEEGIETQYFAEL
Retrocopy DLLRIIQLGLTFMNEQGEYPPRTPTRQLNFKFNLTEDMYAQDSTELLTTSDIQF*KHEEEGIETQYFAEL

Parental  LMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRL-FFPVIYDVKYLMKSCKNLKGG
          LMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFF.IL.L.FFPVIYDVKYLMKSCKNLKGG
Retrocopy LMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFKILQL>FFPVIYDVKYLMKSCKNLKGG

Parental  LQ-EVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYCGHLYGLGSGSSYVQNGTGNAY
          LQ.EVAEQ.ELERIGP.HQAGSD.LL.G.AFFKMREMFFEDHIDDAKY.GHLYGLGSGSSYVQNGTGNAY
Retrocopy LQ<EVAEQ*ELERIGPRHQAGSDALLIGIAFFKMREMFFEDHIDDAKYYGHLYGLGSGSSYVQNGTGNAY

Parental  EEEANKQS
          EEE.NKQS
Retrocopy EEEVNKQS

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	20.86 RPM
SRP051959_heart	0.53 RPM	17.84 RPM
SRP051959_kidney	1.73 RPM	23.83 RPM
SRP051959_liver	1.17 RPM	24.48 RPM
SRP051959_lung	1.32 RPM	22.27 RPM
SRP051959_lymph_node	1.83 RPM	25.48 RPM
SRP051959_skeletal_muscle	0.74 RPM	17.19 RPM
SRP051959_spleen	1.49 RPM	24.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_720 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_720 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_720 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000677	4 retrocopies	retro_chof_1431, retro_chof_1581, retro_chof_822, retro_chof_963,
Callithrix jacchus	ENSCJAG00000011795	1 retrocopy	retro_cjac_720 ,
Felis catus	ENSFCAG00000000591	1 retrocopy	retro_fcat_1889,
Homo sapiens	ENSG00000198791	2 retrocopies	retro_hsap_211, retro_hsap_4851,
Macaca mulatta	ENSMMUG00000001873	1 retrocopy	retro_mmul_2592,
Monodelphis domestica	ENSMODG00000019055	2 retrocopies	retro_mdom_1898, retro_mdom_802,
Mustela putorius furo	ENSMPUG00000017972	1 retrocopy	retro_mputfur_1596,
Nomascus leucogenys	ENSNLEG00000002489	2 retrocopies	retro_nleu_1860, retro_nleu_2373,
Oryctolagus cuniculus	ENSOCUG00000014589	1 retrocopy	retro_ocun_118,
Otolemur garnettii	ENSOGAG00000006324	2 retrocopies	retro_ogar_1883, retro_ogar_505,
Pongo abelii	ENSPPYG00000018385	2 retrocopies	retro_pabe_3771, retro_pabe_428,
Sarcophilus harrisii	ENSSHAG00000011828	2 retrocopies	retro_shar_103, retro_shar_631,
Ictidomys tridecemlineatus	ENSSTOG00000009175	2 retrocopies	retro_itri_1729, retro_itri_1730,