RetrogeneDB ID: retro_chof_1400

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_283004:688..1707(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MKKS
• Ensembl ID: ENSCHOG00000000551
• Aliases: None
• Description: McKusick-Kaufman syndrome [Source:HGNC Symbol;Acc:7108]

Sequence

>retro_chof_1400
AAGTCTGAGGTCTGTGGTTGTTGAGTCCCAGTCGACTTTAGTAGTACTCACATCTTCCTTTGTTTGGTATGCATTAATTA
AATTAATAGTAAACCTGTCTGTGTGTTCACCAGCAAGGACGTAGATCACATTGGTGCTTTGATTCTGAAAGCCTTTGTGT
TTATAATTCCAGAAAAGGCTGAAGAATACATATTTAAGGAGACTATAATTATACCTTTAAAAGGTCAAAGAGTTATAGAT
TCCACTTTGTTACCTGGAATACTCAATGAAATATCAGAAGTTCAGTTGATGAGGATGTTACCCATCAAAAAATCAAGTGC
CTTCAAGGTGGCACTCTTTGGTACACCTTTATCTGGAGTCCTTTCTGACACTGAAGAAGGAATTGTGGTGATCAGTTATG
AAGTTTCTCTTAAAAATGCAGTCCTGGACTAGTTGTTTAACCTAGGAAGGAAGCTGGTTATTGACCACATAGATCTTGTC
ATGTGCCCAAAAGTCATATACCCATCTTTAAATTGTTTCTCAATGTGCATCATTATATTGTTGCCATAAACAGAGTGGGA
GAGGCCCTGAAGAAAATGACAAGAACACAGCCTATTGGTTCTCTGAGCTCAGTCTTTCCTAATAGTTATGGAAGTGTGAA
AGATTTATGCTTTGCAAAATTTTACTCCGAACATTTTTTTCATCTTGTTCCTAATGAAGTGACTGTCTGCAGTTTGGTCC
TCTGTAACAGAAATGACACTGCCTGGGATGAGCTGAAATTCACATGTCAAACAGCACTGCATGTCTTGCAGTTAACAATC
AACCAACCATCAGTTTTTTGGGGGAGGTGGCTATTCTGATACTTCTTTAGCTGCATATATGAGACACAAGATTCTTAACC
AGTCAGAAAGCATTCTCAAAGATGGTGGATGTACTCAAACAGAACATCAACTGATTGTGGAAACATTTTGCAATCTCTAG
AATCTCTCACTGGCACTTCAGAACATGACAGAGGTGAAATTCTCTTTGATGTGAAGTAT

Alignment

ORF - retro_chof_1400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.99 %
• Parental protein coverage: 60.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KSEVCGCHVPVDFGSTHILLCLVR-SILTSKPACMLTTKEIDHISTLILRAFLLTIPEKAEEHIILGKSI
          KSEVCGC.VPVDF.STHI.LCLV......SKP.C..T.K..DHI..LIL.AF...IPEKAEE.I.....I
Retrocopy KSEVCGC*VPVDFSSTHIFLCLVCIN*INSKPVCVFTSKDVDHIGALILKAFVFIIPEKAEEYIFK-ETI

Parental  IVPLKGQRVIDSTLLPGILIEISEVQLMRMLPIKKSSALKVALFCASLSGDLSDTGEGTVVVSYGVSLEN
          I.PLKGQRVIDSTLLPGIL.EISEVQLMRMLPIKKSSA.KVALF...LSG.LSDT.EG.VV.SY.VSL.N
Retrocopy IIPLKGQRVIDSTLLPGILNEISEVQLMRMLPIKKSSAFKVALFGTPLSGVLSDTEEGIVVISYEVSLKN

Parental  AVLDQLLNLGRQLISDHVDLVMCQKVIHPSL-KQFLSTHH-IIAIDRVGVALMEPLKKMTGTQPIGSLSS
          AVLD.L.NLGR.L..DH.DLVMC.KVI.PSL.K.FL..HH.I.AI.RVG....E.LKKMT.TQPIGSLSS
Retrocopy AVLD*LFNLGRKLVIDHIDLVMCPKVIYPSL<KLFLNVHHYIVAINRVG----EALKKMTRTQPIGSLSS

Parental  VSPSSYGSVKDLCFAKFGSKHFFHLVPNEVTVCSLLLCNRNETAWDELKRTCQTALHVLQLTIKQPSVLL
          V.P.SYGSVKDLCFAKF.S.HFFHLVPNEVTVCSL.LCNRN.TAWDELK.TCQTALHVLQLTI.QPSV..
Retrocopy VFPNSYGSVKDLCFAKFYSEHFFHLVPNEVTVCSLVLCNRNDTAWDELKFTCQTALHVLQLTINQPSVFW

Parental  -GGGCTETHLAAYIRHKILNQPESILKDGGYTQTELQLTAEAFCGV-LESLTDSLERDGGKILIDMKH
          .GGG...T.LAAY.RHKILNQ.ESILKDGG.TQTE.QL..E.FC...LESLT...E.D.G.IL.D.K.
Retrocopy >GGGYSDTSLAAYMRHKILNQSESILKDGGCTQTEHQLIVETFCNL<LESLTGTSEHDRGEILFDVKY

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1400 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000551	1 retrocopy	retro_chof_1400 ,