RetrogeneDB ID: retro_chof_1175

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_218493:554..1250(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000006159
• Aliases: None
• Description: None

Sequence

>retro_chof_1175
TCTGCTCTCTCCATCTTGTGTCTAGATCTCTGACAGGGATCCTGGATCTAGGAATTAAAGATCTCATTGTGCTATATTGC
CAGATTTTCTTACTGTTTGCTCTTCTTACTTTAATCACATCTGTGACTACCTCATTGATGAACTCATTTAAATGTTCCTA
AGTTTTCTGAAAGAAGAAGGAACGAATGAGAAAAGGCAAAAGCTTGTGCAAAACAAAGAAGAGGCACAGAGTGAAAAGGC
CAGCAGATACAGAGAAGTTTTGAAACCTTACTAGGAAATGAAATTTAAAAAAACTGGAAAAGTGCTTTCATCAGATGATG
GGTGAAACCTGGAAGTTAAGCGATGGTCACAAACTTGGGGGTGATGAGTTGGTACTTGAAAGTGCCAGCCAGACATCTTC
TGAAACTTCAAGCAGAGAAGCTGCAGAGACAAAATTTGCCTAAGCCTGTAACCAAACTTTCACGACCTCCTGAACAGCCC
ACACAGAAGAAGTTTCTTGATTTACCTGAAGAAACTCCTAAAACAGACAAAGAAGTAGTTACTGTTGCTCTCAGATATCC
AACTGGCAGTGTCCTGAAGAGAAGGTTTTTGAAGTCTTACAGTTCACAGGTCTCATTTGATTGACTGGTGAAAACTCGTT
ACTTCACATCCCCAGATAGCCTTTCTACTTCCTTTCCCAGAAGACCTCTGGAATTG

Alignment

ORF - retro_chof_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.24 %
• Parental protein coverage: 86.35 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SALPLLCLELRRG-IPDLGIKDLVLLCGRIFLLLALLTLIISVTTSWLNSFKSSQV-YLKEEEEEKNGKR
          SAL..LCL.L..G.I.DLGIKDL..L...IFLL.ALLTLI.SVTTS..NSFK.S.V..LKEE....N.KR
Retrocopy SALSILCLDL*QG<ILDLGIKDLIVLYCQIFLLFALLTLITSVTTSLMNSFKCS*V<FLKEEGT--NEKR

Parental  QKLVLNRQQETQSEKASRYIEKVLKPHQEMK-LKKLEERFYQMSGETWKLSNGHKLGGDEGLVLENASQT
          QKLV.N...E.QSEKASRY.E.VLKP..EMK.LKKLE..F.QM.GETWKLS.GHKLGGDE.LVLE.ASQT
Retrocopy QKLVQNKE-EAQSEKASRYRE-VLKPY*EMK>LKKLEKCFHQMMGETWKLSDGHKLGGDE-LVLESASQT

Parental  SETSNREAA-RRRNLPEPVTKLSRPPDQPT-KKXXXXXXXXXXXXXXVVTVALRCPSGSMLK-RRFKTCX
          S.......A..R.NLP.PVTKLSRPP.QPT.KK..............VVTVALR.P.GS.LK.R..K...
Retrocopy SSETSSREA>QRQNLPKPVTKLSRPPEQPTQKKFLDLPEETPKTDKEVVTVALRYPTGSVLKRRFLKSYS

Parental  XXV-LDWMMKIGYHTSLYSLSTSFPRRPLEV
          ..V..D...K..Y.TS..SLSTSFPRRPLE.
Retrocopy SQVSFD*LVKTRYFTSPDSLSTSFPRRPLEL

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_1175 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001600	2 retrocopies	retro_amel_1272, retro_amel_1326,
Choloepus hoffmanni	ENSCHOG00000006159	4 retrocopies	retro_chof_1161, retro_chof_1175 , retro_chof_1383, retro_chof_1500,
Myotis lucifugus	ENSMLUG00000016846	1 retrocopy	retro_mluc_606,