RetrogeneDB ID: retro_pmar_20

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL494382:777..1284(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ctdsp2
• Ensembl ID: ENSPMAG00000009544
• Aliases: None
• Description: CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2 [Source:ZFIN;Acc:ZDB-GENE-030131-184]

Sequence

>retro_pmar_20
AAACCTTGGGCAACTGGCAAGAAGACACTGGTACTAGATTTAGATGAAACATTAGTTCATAGCAGTTTCAAACCTCCAGC
AAAACCAGATATAGTTTTACCAGTAGAAATTGAAGGCAATGTTTGCAATGTATTTGTACTAATTAGACCTGGAACTGAAT
TCTTCTTACAACGATTAGCCAAATGCTATGAAATAGTAATTTACACAGCGAGTTTGAGTAAATACGCAGATCCACTAATT
GACATCCTTGATAACAAACCCCAAAAAATAATAGACTATCGCCTCTTCCGAGAGCACTGTACTTTTTTCCAGGGTGTATT
TATAAAAGACATGTCTCTCCCTGGCAGAGCACTTTAAGACTCAATTATAATAGACAACTCCCCCACAAGTTACGCTTTTC
ATTAAGAAAACGCACTCCCTTTCCTTTCTTGGTATGATGACCCAAAAGATCGGTGTTTATTTGAGTTGATACCTTTGCTT
GAATCACTGGCCGAAGTGGACGATGTG

Alignment

ORF - retro_pmar_20 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.66 %
• Parental protein coverage: 68.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RPLDEGKKCMVIDLDETLVHSSFKPIENADFIIPVEIEGTTHQVYVMKRPFVDEFLQRMGELFECVLFTA
          .P...GKK..V.DLDETLVHSSFKP....D...PVEIEG....V.V..RP....FLQR.....E.V..TA
Retrocopy KPWATGKKTLVLDLDETLVHSSFKPPAKPDIVLPVEIEGNVCNVFVLIRPGTEFFLQRLAKCYEIVIYTA

Parental  SLAKYADPVADLLDR--WGVFRVRLFRESCVFHHGSYVKDLSRLGRDLSQTIIIDNSPASYIFHPENAVP
          SL.KYADP..D.LD.........RLFRE.C.F..G...KD.S..GR.L...IIIDNSP.SY.FH.ENA.P
Retrocopy SLSKYADPLIDILDNKPQKIIDYRLFREHCTFFQGVFIKDMSLPGRAL*DSIIIDNSPTSYAFH*ENALP

Parental  VGSWFDDMSDMELLDLIPLFEELGKTEDI
          ..SW.DD..D..L..LIPL.E.L....D.
Retrocopy FLSWYDDPKDRCLFELIPLLESLAEVDDV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Petromyzon marinus was not studied using RNA-Seq expression data.

ChIP-Seq

Petromyzon marinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pmar_20 retrocopy.

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_20 was not experimentally validated.

Homology

Retrocopy orthology:

Petromyzon marinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005618	1 retrocopy	retro_chof_1918,
Callithrix jacchus	ENSCJAG00000006503	2 retrocopies	retro_cjac_3087, retro_cjac_919,
Homo sapiens	ENSG00000175215	2 retrocopies	retro_hsap_4315, retro_hsap_4319,
Macaca mulatta	ENSMMUG00000005321	2 retrocopies	retro_mmul_2208, retro_mmul_764,
Mus musculus	ENSMUSG00000078429	1 retrocopy	retro_mmus_612,
Nomascus leucogenys	ENSNLEG00000017164	2 retrocopies	retro_nleu_1741, retro_nleu_3079,
Petromyzon marinus	ENSPMAG00000009544	2 retrocopies	retro_pmar_20 , retro_pmar_27,
Pongo abelii	ENSPPYG00000004711	14 retrocopies	retro_pabe_1708, retro_pabe_1739, retro_pabe_1740, retro_pabe_1742, retro_pabe_1746, retro_pabe_1762, retro_pabe_2402, retro_pabe_2592, retro_pabe_3202, retro_pabe_3205, retro_pabe_3221, retro_pabe_3237, retro_pabe_3554, retro_pabe_3578,
Pan troglodytes	ENSPTRG00000005155	7 retrocopies	retro_ptro_2587, retro_ptro_2589, retro_ptro_2590, retro_ptro_2592, retro_ptro_2594, retro_ptro_2958, retro_ptro_3054,