RetrogeneDB ID: retro_cjac_3301

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:48131793..48132881(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033484
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: METT5D1
• Ensembl ID: ENSCJAG00000006142
• Aliases: None
• Description: None

Sequence

>retro_cjac_3301
AAAGAATACAAACTACAGCAGAAAAGTATAAAGACTATGAAGCCCAGATCTCAAGATAGAGATTTTGAAAACCTGACTAA
ATTACATATTTCAGTAATGGTGGATGAAGTTGGTCATTGTTTGTCACCCCAAAAAGGACAGACTTTTCTAGATATGGCAT
TTGGTTTGGGAGGGCACACGAAAGCTATTCTACAGAAGGAGTCAGATATTGTTCTGTACACTTTGGATAGAGACCCAGCA
GCTTACGCATTAGCTGAACATCATTTGAAGCTGTCTCCTAAACAAATCCGAGCTATGCTGGGCCAGTTCAGCCAGGCAGA
AGCCTTATTAATGAAAGCTGGAGTACAGCTAGGGACTTTTGATGGAGTTCTTATGGATCTTGGATGTTCCTACATGCAAC
TTGATACTCCTAAAAGAGGTTTTTCCCTTCAGAAAGATGGCCCCTTGAACATGAGAATGGATGGTGGCAGGTACCCCGAT
ATGCCCACTGCTGGTGATGTTGTAAATGCTTTAAATCAACAGGCACTTGCATCTATCCTGAGAACATACCAGGAAGAAAA
GCATGCCAAGAAAATCACTTCAGCAATTGTTCAGGCACGCAGTATCTACCCCATCACCAGAACCCAGCAGCTTGCCAGCA
TCATCGCAGGTGCATTTTCTCTCTCTGCTATTTATGAATGAAAAGACTTGGTACAGCAATTTACCCAAATTGCCACCAAG
ACTTCCCAGGCTCTTCGCATATTTGGGAACAATGAGCTCAATGAACTCTACACAGGACTAAAGACAGCTCAGAAGTTTCT
GAGACCTGGTGATTGCCTTGTTGCCCTCTCCTTCCATTCACTAGAGGATTGCATCATCAAAAGATTTTTGCTTGGAATAA
GCATGAAAGAAAGATTTAACCTAAGGGTCAGACAGCAAGTGATGAAAACATCACAATTGGGTTCAGATCACGGAAGCACA
GAAGTCTCTATGAGAAGAGTTCCTTTTATGTGGGACTTGATACATAAGAAGGTACTTAATCCACAAGTTCAAGATGTACA
AGAAACCTCAGACGGTGCTCAGCCAAGCTTAGAGTGGCTATCAAATTA

Alignment

ORF - retro_cjac_3301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.47 %
• Parental protein coverage: 90.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KEYEAHEQTYQTQAQESHRSQDRNFETMVKLHIPVMVDEVVHCLSPQKGQIFLDMTFGSGGHTKAILQKE
          KEY........T......RSQDR.FE...KLHI.VMVDEV.HCLSPQKGQ.FLDM.FG.GGHTKAILQKE
Retrocopy KEYKLQQKSIKTMKP---RSQDRDFENLTKLHISVMVDEVGHCLSPQKGQTFLDMAFGLGGHTKAILQKE

Parental  SDIVLYALDRDPTAYALAEHLSELYPKQIRAMLGRFSQAETLLMKAEVQPGTFDGVLMDLGCSSMQLDTS
          SDIVLY.LDRDP.AYALAEH...L.PKQIRAMLG.FSQAE.LLMKA.VQ.GTFDGVLMDLGCS.MQLDT.
Retrocopy SDIVLYTLDRDPAAYALAEHHLKLSPKQIRAMLGQFSQAEALLMKAGVQLGTFDGVLMDLGCSYMQLDTP

Parental  ERGFSLRKDGPLDMRMDGDRYPDMPTAADVVNALDQQALASILRAYGEEKHAKKIASAIVQARSIYPITR
          .RGFSL.KDGPL.MRMDG.RYPDMPTA.DVVNAL.QQALASILR.Y.EEKHAKKI.SAIVQARSIYPITR
Retrocopy KRGFSLQKDGPLNMRMDGGRYPDMPTAGDVVNALNQQALASILRTYQEEKHAKKITSAIVQARSIYPITR

Parental  TQQLASIIAGAFPPSAIYARKDLLQRSTHIATKTFQALRIFVNNELNELHTGLKTAQKFLRPGGRLVALS
          TQQLASIIAGAF..SAIY..KDL.Q..T.IATKT.QALRIF.NNELNEL.TGLKTAQKFLRPG..LVALS
Retrocopy TQQLASIIAGAFSLSAIYE*KDLVQQFTQIATKTSQALRIFGNNELNELYTGLKTAQKFLRPGDCLVALS

Parental  FHSLEDRIVKRFLLGISMTERFNLSVRQQVMKASRLDSDHENVEVSMRRAPLMWELIHKKVLSPQSRDVQ
          FHSLED.I.KRFLLGISM.ERFNL.VRQQVMK.S.L.SDH...EVSMRR.P.MW.LIHKKVL.PQ..DVQ
Retrocopy FHSLEDCIIKRFLLGISMKERFNLRVRQQVMKTSQLGSDHGSTEVSMRRVPFMWDLIHKKVLNPQVQDVQ

Parental  D-NPRGRSAKLRAAIKL
          ..N.R..SAKLR.AIKL
Retrocopy E<NLRRCSAKLRVAIKL

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	4.15 RPM
SRP051959_heart	0.00 RPM	6.38 RPM
SRP051959_kidney	0.02 RPM	7.48 RPM
SRP051959_liver	0.00 RPM	11.03 RPM
SRP051959_lung	0.00 RPM	6.93 RPM
SRP051959_lymph_node	0.00 RPM	7.76 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.31 RPM
SRP051959_spleen	0.00 RPM	8.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3301 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3301 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1123
Pan troglodytes	retro_ptro_680
Macaca mulatta	retro_mmul_870

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006142	2 retrocopies	retro_cjac_3301 , retro_cjac_4047,
Homo sapiens	ENSG00000169519	2 retrocopies	retro_hsap_1123, retro_hsap_4656,
Macaca mulatta	ENSMMUG00000013616	1 retrocopy	retro_mmul_870,
Nomascus leucogenys	ENSNLEG00000017865	2 retrocopies	retro_nleu_1093, retro_nleu_187,
Oryctolagus cuniculus	ENSOCUG00000014291	1 retrocopy	retro_ocun_536,
Pongo abelii	ENSPPYG00000003399	1 retrocopy	retro_pabe_3617,
Pan troglodytes	ENSPTRG00000003461	1 retrocopy	retro_ptro_680,