RetrogeneDB ID: retro_cjac_2802

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:32086766..32087446(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CWC15
• Ensembl ID: ENSCJAG00000004188
• Aliases: None
• Description: CWC15 spliceosome-associated protein homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26939]

Sequence

>retro_cjac_2802
TTGACAACCACAGCCAGGCCAACCTTTGAACCTGCAAGGGGTGGAAGAGGCAAAGGAGAAGGTGATTTGAGCCAACTTTC
AAGCAGTATTCAAGCAGAGAGCTACCTTTTCATACAAAGATAAAACACAGACAGCGCTCAGGATGCCCCTGAAGAGGTTT
GTAACCGTGACTTCAGGAGAGAGTTGGGAGAAAGAGAGAGAACTGCCGCAACAGAGAAAAACAGCGGTCGTCCAGCCCGA
GAACAGACAACCTCCTCTTCAGTGTCAAAAAAGCCACGGTTAGACCAGATTCCTGCTGCCAACCTTCATGCCAATTACCC
TCTAACAGATGAGGAAGGTGAGGATTTTGAAGAACAAAGTGACGATGATGATACTGCAGCTCTTGTTGCAGAACTGGAAA
AATTTTAAAAAGAAAGAGCTGAAGAGCAGGCCAGGAAGGAACAAGAACAAAAAGCTGAAGAATCGAGGACTCATACGGAA
AACACTCTGAGCGCAAACCCTCTCCTTAATCTCACTGGCCCATCCCAGCCTCAGACCAACTTCAAAGGTAAAAGAAGGTG
GGATGATGATTTTGTCTTCAACAACTGTGCAAAGGTGTAGATGACCAGAAGAAAGACAAAAGATTTGTAAATGACACACT
GCGATCTGAATTTCACAAAAAGTTCATGGAGAAACGTATT

Alignment

ORF - retro_cjac_2802 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.35 %
• Parental protein coverage: 99.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTTAARPTFEPARGGRGKGEGDLSQLSKQYSSRDLPSHTKIKYRQT--TQDAPEEVRNRDFRRELEERER
          .TT.ARPTFEPARGGRGKGEGD...LS...SS....S...I....T...QDAPEEV.NRDFRREL.ERER
Retrocopy LTTTARPTFEPARGGRGKGEGD---LSQLSSSIQAESYLFIQR*NTDSAQDAPEEVCNRDFRRELGERER

Parental  AAAREKNRDRPTREHTTSSSVSKKPRLDQIPAANLDADDPLTDEEDEDFEEESDDDDTAALLAELEKIKK
          .AA.EKN..RP.RE.TTSSSVSKKPRLDQIPAANL.A..PLTDEE.EDFEE.SDDDDTAAL.AELEK..K
Retrocopy TAATEKNSGRPAREQTTSSSVSKKPRLDQIPAANLHANYPLTDEEGEDFEEQSDDDDTAALVAELEKF*K

Parental  ERAEEQARKEQEQKAEEERIRMENILSGNPLLNLTGPSQPQANFKVKRRWDDDVVFKNCA-KGVDDQKKD
          ERAEEQARKEQEQKAEE.R...EN.LS.NPLLNLTGPSQPQ.NFK.KRRWDDD.VF.NCA.KGVDDQKKD
Retrocopy ERAEEQARKEQEQKAEESRTHTENTLSANPLLNLTGPSQPQTNFKGKRRWDDDFVFNNCA<KGVDDQKKD

Parental  KRFVNDTLRSEFHKKFMEKYI
          KRFVNDTLRSEFHKKFMEK.I
Retrocopy KRFVNDTLRSEFHKKFMEKRI

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	0.00 RPM	21.88 RPM
SRP051959_heart	0.00 RPM	46.74 RPM
SRP051959_kidney	0.00 RPM	40.82 RPM
SRP051959_liver	0.00 RPM	39.34 RPM
SRP051959_lung	0.00 RPM	42.51 RPM
SRP051959_lymph_node	0.02 RPM	37.56 RPM
SRP051959_skeletal_muscle	0.02 RPM	92.86 RPM
SRP051959_spleen	0.02 RPM	47.14 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2802 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2802 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2802 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007913	1 retrocopy	retro_btau_703,
Canis familiaris	ENSCAFG00000004134	6 retrocopies	retro_cfam_1329, retro_cfam_2123, retro_cfam_503, retro_cfam_537, retro_cfam_61, retro_cfam_805,
Callithrix jacchus	ENSCJAG00000004188	1 retrocopy	retro_cjac_2802 ,
Cavia porcellus	ENSCPOG00000006249	1 retrocopy	retro_cpor_708,
Echinops telfairi	ENSETEG00000006649	1 retrocopy	retro_etel_647,
Felis catus	ENSFCAG00000007826	1 retrocopy	retro_fcat_1416,
Myotis lucifugus	ENSMLUG00000002032	3 retrocopies	retro_mluc_102, retro_mluc_2143, retro_mluc_2478,
Mus musculus	ENSMUSG00000004096	2 retrocopies	retro_mmus_2482, retro_mmus_593,
Ornithorhynchus anatinus	ENSOANG00000010404	1 retrocopy	retro_oana_5,
Otolemur garnettii	ENSOGAG00000001686	2 retrocopies	retro_ogar_2476, retro_ogar_456,
Rattus norvegicus	ENSRNOG00000008490	3 retrocopies	retro_rnor_2452, retro_rnor_251, retro_rnor_476,
Sarcophilus harrisii	ENSSHAG00000016534	5 retrocopies	retro_shar_26, retro_shar_333, retro_shar_447, retro_shar_596, retro_shar_768,
Tarsius syrichta	ENSTSYG00000000407	1 retrocopy	retro_tsyr_1585,