RetrogeneDB ID: retro_etel_1142

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_217531:4012..4798(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBLCP1
• Ensembl ID: ENSETEG00000000170
• Aliases: None
• Description: ubiquitin-like domain containing CTD phosphatase 1 [Source:HGNC Symbol;Acc:28110]

Sequence

>retro_etel_1142
GTTCCTCTGATCATAAAGTGGGGTGGACAGGAATATTCAGTGACCACGCTATCCAAAGATGATACTGTACAAGATCTCAA
ACAGTTTCTCAAACCCTTACAGGAGTCCTGCCAGAGTGCCAGAAGTTACTTGGACTCAAAGTTAAAGGCAAGCCTGCAGA
AAAGGTTGTTAAGCATGGAGCTCTCAAACTGAAACCAAATACTAAAATCACGACGATGGTAACTCATGAGGAGAGCTTAG
AAGTTGTCTTAGGTCCACCCCCTGACATTGATGACTTTGCCAATGACTTTGATATTGAAGATGAAGTAGTTGAAGTGGAG
AGCAGAGAAGAAAACCTCCTGGAAATCTCTCACAGAATTAAAGAGTACAAAGTGGAAATTTTAAATCCTCCCAGGGAAGG
GAAAAAACTTTTGGTACTAGATGTTGATCATACTTTGTTTGACCACAGGTCTTGTGCAGAGACTGGGGTAGAATTGTTGT
GGCCATATCTTCATGAATTCCTAACATCTTCCTATGAGGAGTATGCATTGTTATTTGGTCTGCAACAACTATGAAGTGGA
CTGAAGCTAAAATCAAAGAGCTGGTGTGAATACAAATGCGAACGAACTATGAAATCACCCTTACATTGGACAGCGCTGCT
ATGACAACAGTGCTCATCCCAAGGCGAGGACCATAGACATAAAACCTCTTGGTGTCATATGGGGAAAGTTTTCAGAGTTT
CACAGCAAAAAGAACACCATTATGTTTGATGACATAGGAAGAAATTTTCCAATGAACTCACAGGAT

Alignment

ORF - retro_etel_1142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.2 %
• Parental protein coverage: 82.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VPLIVKWGGQEYSVTTLSEDDTVLDLKQFLR-TPTGVLPERQKLLGL-VKGKPAENDVKLGALKLKPNTK
          VPLI.KWGGQEYSVTTLS.DDTV.DLKQFL..T.TGVLPE.QKLLGL.VKGKPAE..VK.GALKLKPNTK
Retrocopy VPLIIKWGGQEYSVTTLSKDDTVQDLKQFLK<TLTGVLPECQKLLGLKVKGKPAEKVVKHGALKLKPNTK

Parental  IMMMGTREESLEDVLGPPPDNDDVVNDFDIEDEVVEVENREENLLKISRRVKEYKVEILNPPREGKKLLV
          I..M.T.EESLE.VLGPPPD.DD..NDFDIEDEVVEVE.REENLL.IS.R.KEYKVEILNPPREGKKLLV
Retrocopy ITTMVTHEESLEVVLGPPPDIDDFANDFDIEDEVVEVESREENLLEISHRIKEYKVEILNPPREGKKLLV

Parental  LDVDYTLFDHRSCAETGVELMRPYLHDFLTSAYEDYD-IXXXXATNMKWIEAKMKELG-VSTNANYKITF
          LDVD.TLFDHRSCAETGVEL..PYLH.FLTS.YE.Y..I....AT.MKW.EAK.KEL.......NY.IT.
Retrocopy LDVDHTLFDHRSCAETGVELLWPYLHEFLTSSYEEYA<IVIWSATTMKWTEAKIKELV*IQMRTNYEITL

Parental  MLDSAAMITVHTPRRG-LIDVKPLGVIWGKFSEFYSKKNTIMFDDIGRNFLMNPQN
          .LDSAAM.TV..PRRG..ID.KPLGVIWGKFSEF.SKKNTIMFDDIGRNF.MN.Q.
Retrocopy TLDSAAMTTVLIPRRG<TIDIKPLGVIWGKFSEFHSKKNTIMFDDIGRNFPMNSQD

Legend:

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

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1142 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007691	1 retrocopy	retro_chof_51,
Echinops telfairi	ENSETEG00000000170	1 retrocopy	retro_etel_1142 ,
Microcebus murinus	ENSMICG00000010060	2 retrocopies	retro_mmur_1083, retro_mmur_1319,
Myotis lucifugus	ENSMLUG00000006359	1 retrocopy	retro_mluc_1367,
Monodelphis domestica	ENSMODG00000008063	2 retrocopies	retro_mdom_1251, retro_mdom_1351,
Mustela putorius furo	ENSMPUG00000013396	1 retrocopy	retro_mputfur_1098,
Mus musculus	ENSMUSG00000041231	1 retrocopy	retro_mmus_762,
Oryctolagus cuniculus	ENSOCUG00000002224	1 retrocopy	retro_ocun_1036,
Tupaia belangeri	ENSTBEG00000008983	1 retrocopy	retro_tbel_41,
Tursiops truncatus	ENSTTRG00000005876	1 retrocopy	retro_ttru_761,