RetrogeneDB ID: retro_chof_2697

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_983:16578..17663(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS27
• Ensembl ID: ENSCHOG00000002565
• Aliases: None
• Description: mitochondrial ribosomal protein S27 [Source:HGNC Symbol;Acc:14512]

Sequence

>retro_chof_2697
GATCTAGCATCTTTAATGGATAAAACATATGAAAGAAAGTTGGCTATTACTTCTTTGACAATATCACGGTTTGCAAACAT
CTCATCTCAAGAAGACAGAGATCCGGCAGAGTATTACCTTTACAAATTTCAACACAGCCCCAACTGCTGGTACCTGAGAG
ACGGACGATCCCCACCTGGATTAGGCAGTGTCTAAAATACAGTGCACAAGACAAAACCTCATATACCTTTGTAAATAAGG
TTCAATATGGAATTTTTCCAGATAACTTTACATTCAATTTACTGATGGATTATTTCATTTAAAAAGAAAACTATGAAGAT
GCATTATCTGTGGTTTTTGAGATCATGATGCAAGAAACCTTTGAAGTGCCTTCCACTCAACTTGTCTCTCTCTCTGTTTT
ATACCATTGCCTGGCAAAGAAGACAGACTTTGGTTGGGAAGAGAAGAATTTTGGTGTATCCCTACAGCTCCCAGGCCTAA
AACAAGAGAACACTATGGGTTTGAGTTCCCAGCTGTATGGCTTTGCACTTCTTAGGAAGGTGGAGTTGTTTCAAGGGCTG
TGGGCAATATACCACAAAATGCCTCTGATGTGGAAACCAGGGTATCTTGACAGAACCCTTCAAGTGATGGAGAAAGTGGC
GGCCTCCCCAGAAGACATAAAGCTGTATCAAGAAGTGCTGGCTATGCTGGACAGAGTGCTGCAGGCTCTGATTTCTGCAG
CCAATGTGTCTTCAGAGGAACAGTCCCAAAGAAGTGAAGACAAACAGGGTTCAGAAGAACTGGTGGAGCAGTCAGACATA
GAAGACACAGAACAGTCTAAACTTCCCCAATACCTGAAACAATTTAAGGCCTTACATTCTAAGCTACAGGCTCTGGGCAA
GGTTGATTCAAGAAGCCTTTTGACTCTGACCACCCAGCTTGTCAAGGAGAAGCTCCCCGCCAACGAAGCAGAGGACATCA
CCAATGACAAGCAGAAACTGCAGCAGTGGAACCAGGAGTGGGTACAGTTGATTCAGAGGGAACAGTACCAGAGGGAGAAA
GTAAAACAGGAGCATCAGGCTCGGAGAGCTGTAAAGGCATCTGCC

Alignment

ORF - retro_chof_2697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DLASLMDKTYERKLPVSSLTISRFVDNISSREEIDHAEYYLYKFRHSPNCWYLRDW-TIHTWIRQCLKYG
          DLASLMDKTYERKL...SLTISRF..NISS.E..D.AEYYLYKF.HSPNCWYLRD..TI.TWIRQCLKY.
Retrocopy DLASLMDKTYERKLAITSLTISRFA-NISSQEDRDPAEYYLYKFQHSPNCWYLRDG<TIPTWIRQCLKYS

Parental  AQDKALYTLVNKVQYGIFPDNFTFNLLMDYFIKKENYKDALSVVFEIMMQEAFEVPSTQLLSLDVLYHCL
          AQDK..YT.VNKVQYGIFPDNFTFNLLMDYFI.KENY.DALSVVFEIMMQE.FEVPSTQL.SL.VLYHCL
Retrocopy AQDKTSYTFVNKVQYGIFPDNFTFNLLMDYFI*KENYEDALSVVFEIMMQETFEVPSTQLVSLSVLYHCL

Parental  AKKTDFSWEEEKNFGASLLLPGLKQENTVGLSSQLYGFALLGKVELLQGLRAVYHNMPLMWKPGYLDRAL
          AKKTDF.WEE.KNFG.SL.LPGLKQENT.GLSSQLYGFALL.KVEL.QGL.A.YH.MPLMWKPGYLDR.L
Retrocopy AKKTDFGWEE-KNFGVSLQLPGLKQENTMGLSSQLYGFALLRKVELFQGLWAIYHKMPLMWKPGYLDRTL

Parental  QVMEKVAASPEDVKLCQEALNVLDTVLQSLISPADGSSEEQPQGGKDNQGSEELLEQLDIEEIEQAKLPQ
          QVMEKVAASPED.KL.QE.L..LD.VLQ.LIS.A..SSEEQ.Q...D.QGSEEL.EQ.DIE..EQ.KLPQ
Retrocopy QVMEKVAASPEDIKLYQEVLAMLDRVLQALISAANVSSEEQSQRSEDKQGSEELVEQSDIEDTEQSKLPQ

Parental  YLEKFKALHSKLQALGKVESGSLLTLTTQLVKEKLPTCEAEDITNYEQKLQQWNLERVQLIQREQEQREK
          YL..FKALHSKLQALGKV.S.SLLTLTTQLVKEKLP..EAEDITN..QKLQQWN.E.VQLIQREQ.QREK
Retrocopy YLKQFKALHSKLQALGKVDSRSLLTLTTQLVKEKLPANEAEDITNDKQKLQQWNQEWVQLIQREQYQREK

Parental  AKQEHQARRAAKASA
          .KQEHQARRA.KASA
Retrocopy VKQEHQARRAVKASA

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_2697 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002565	1 retrocopy	retro_chof_2697 ,
Myotis lucifugus	ENSMLUG00000007355	1 retrocopy	retro_mluc_771,
Sus scrofa	ENSSSCG00000023818	2 retrocopies	retro_sscr_231, retro_sscr_251,