RetrogeneDB ID: retro_chof_2159

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_5429:20737..21568(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT14
• Ensembl ID: ENSCHOG00000009949
• Aliases: None
• Description: septin 14 [Source:HGNC Symbol;Acc:33280]

Sequence

>retro_chof_2159
AAAGCAACTTGTACATCCTCACAAGTATCTGATGATGAACAGAAACTAAGAAGAGAAAACATTCACTCACTCACTATGTC
TGGTCATGTTGGTTCTGAAAGTTTGCCTGATCAGCTGTTAATAGATCCATTCATCAACACTTCTGTTTTAATATTCTCTG
TATGTGGGAAACTGGAATTGGAAAATCAACACTGAATGACACATTGTTAATACTAATTTTGAAGATTGTGAATCCTCACG
TTTTTACACACAATGTAGACTTAAAGCTCAGACATATGAACTCCAGGAAAGTAACATTCAATTGAAATTGACCGTTGTGT
ATTCAGTAGGATTTGGTGACCAAATAAACAAAGAAGAGAGTTATCAACCTGTAGTTAACTACATAGATGCTCAGTTTGAG
TCCTATCTCCAAGAACTGGAGATTAAACGTTCTCTCTTTAACTACCATGATTCCAGCATCCACGTGTGCCTTTCCTTCAT
TTCACCCGCAGGCCACTCTCTGAAGACACTGATTTCTTAACCATGAAGAGCCTTCACAGTAAAGTGAATATTATACCAGT
AATTGCCAAAGCAGATGCAATTTCTAAAACTGAATTACAGAAGTTCAAGACCAAGTTCCTAAGTGAATTGGTTAGCAGTG
GATATACCAGTTCCCAAAAGATGATGAAACTATTGCTAAAATCAATGCTTCAATGACTGGACATTTAGTATTTGCTATTG
CAGAAAGTATGGAAGAGGTAAAAATTGGAAATAGAATGGTGAAAGCTCGTCATACTCTTGTGCTGTTGTACAAGGGAAAA
TGAAAACAACTGTGACTCTGTAAGCTCCAGG

Alignment

ORF - retro_chof_2159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.6 %
• Parental protein coverage: 75.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KTMCMSTQTPDEEDTQKEENIRCLNLLGHFGFDCLPHQL-VNRSIQQGFSFNILCVGETGIGKSTLIDTL
          K..C.S.Q..D.E.....ENI..L...GH.G...LP.QL.VNRSI.Q.F.FNILC..ETGIGKSTL.DTL
Retrocopy KATCTSSQVSDDEQKLRRENIHSLTMSGHVGSESLPDQL<VNRSIHQHFCFNILCMWETGIGKSTLNDTL

Parental  F-NTNFKDSKSSHFNSNVGLKIQTYKLLESNVQLKLTVVKTVGYGDQLNKEASYRPIVDYIDAQFEAYLQ
          ..NTNF.D..SS.F.....LK.QTY.L.ESN.QLKLTVV..VG.GDQ.NKE.SY.P.V.YIDAQFE.YLQ
Retrocopy L<NTNFEDCESSRFYTQCRLKAQTYELQESNIQLKLTVVYSVGFGDQINKEESYQPVVNYIDAQFESYLQ

Parental  EELKIKRSFFEYHDSRIHVCLYFISPTGHSLKSL-DLLTLKSIDSKVNIIPLIPKADTVCKNDLQTFKNK
          .EL.IKRS.F.YHDS.IHVCL.FISP.GHSLK.L.D.LT.KS..SKVNIIP.I.KAD...K..LQ.FK.K
Retrocopy -ELEIKRSLFNYHDSSIHVCLSFISPAGHSLKTL<DFLTMKSLHSKVNIIPVIAKADAISKTELQKFKTK

Parental  IMNEFISNG-IQIYQFSNEEIIVQVNSSMNGLLPFAVVGSMDEVKVGKRMVRGRQYPWVL-QAENENHCD
          ...E..S.G.I.......E.I....N.SM.G.L.FA...SM.EVK.G.RMV..R.....L...ENEN.CD
Retrocopy FLSELVSSG<IYQFPKDDETI-AKINASMTGHLVFAIAESMEEVKIGNRMVKARHTLVLL>TRENENNCD

Parental  FVKLR
          .V..R
Retrocopy SVSSR

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_2159 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 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003906	1 retrocopy	retro_chof_1543,
Choloepus hoffmanni	ENSCHOG00000008715	5 retrocopies	retro_chof_1371, retro_chof_1579, retro_chof_2198, retro_chof_275, retro_chof_614,
Choloepus hoffmanni	ENSCHOG00000009949	1 retrocopy	retro_chof_2159 ,
Monodelphis domestica	ENSMODG00000003104	1 retrocopy	retro_mdom_93,
Sarcophilus harrisii	ENSSHAG00000007189	1 retrocopy	retro_shar_59,