RetrogeneDB ID: retro_chof_1057

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_191199:2..950(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LCP1
• Ensembl ID: ENSCHOG00000012037
• Aliases: None
• Description: lymphocyte cytosolic protein 1 (L-plastin) [Source:HGNC Symbol;Acc:6528]

Sequence

>retro_chof_1057
CCTAAGGGTGACAGGGATGATGGACCTGCCATTGTCATTGACCTTTCAGGATTTAATGAGCAAAATGACCTGAAGCCTGC
TGGATTCATGCTTCAAGAAGCAGATAAATTGGGCTGTAAACGGTTTGTTACTCCTGCAGATGTGGTTTCAGGCAATCCTA
AACTCAATTTAGCTTTTGTAGCTAATCTCTTTAACACATATCCATGCTTACGTAAACCTAATAATAATGACATCAATATG
AATTTATTGGAAGGAGAGAGCAAGGAAGAGAGGACATTTCAGAATTGGATGAATTCCTTTGGGGTCAACCCATACATTAA
TCATTTGTACAGTGACCTTGCAGATGCTTTAGTGATCTTTCAGCTCTTTGAAATGATCTGAGTGCCAGTCAACTGGAGTC
ATGTCAACAAACCTCCTTATCCTGCCCTTGGAGGGAACATGAAGAAGATTGAAAACTGTAACTGTGCAGTGGAACTTGGG
AAGAATGAGGCTAAATTCTCTTTGGTTGGCATTGCTGGACAGGATCTAAATGAAGGGAATTCAACACTCACACTGGCATT
GGTATGGCAGCTGATGAGACAGTACACATTGAATGTGCTATCAGATCTTGGAGAGGGAGAAAAAGTGAATGATAAAATTA
TTATTAAATGGGTCAATAGTACAAACAAAAATATTTCTATTTCCAGCTTCAAGGACAAATCTATTAGTACTAGCCTACCT
GTTTTAGATTTAACAGATGCCATTGCACCAAATGCAGTACGTCAAGAAATGGTCAAAAGAGAAGACCTTTCGGATGAGGA
CAAGCTGAACAATGCTAAATATGCCATTTTAGTTGCTCGAAAGATCGGTGCCCGGATATATGCACTACCCGATGACCTGG
TAGAAGTGAAACCAAAGATGGTTATGACGGTGTTTCCATGTTTAATGGTAAAAGGACTGAACAGAATA

Alignment

ORF - retro_chof_1057 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.75 %
• Parental protein coverage: 50.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKGNEEGIPAVVIDMSGLREKDDIQRAECMLQQAERLGCRQFVTAADVVHGNPKLNLAFIANLFNRYPAL
          PKG.....PA.VID.SG..E..D...A..MLQ.A..LGC..FVT.ADVV.GNPKLNLAF.ANLFN.YP.L
Retrocopy PKGDRDDGPAIVIDLSGFNEQNDLKPAGFMLQEADKLGCKRFVTPADVVSGNPKLNLAFVANLFNTYPCL

Parental  HKPENQDIDWGALEGETREERTFRNWMNSLGVNPRVNHLYSDLSDALVIFQLYEKIKVPVDWNRVNKPPY
          .KP.N.DI....LEGE..EERTF.NWMNS.GVNP..NHLYSDL.DALVIFQL.E.I.VPV.W..VNKPPY
Retrocopy RKPNNNDINMNLLEGESKEERTFQNWMNSFGVNPYINHLYSDLADALVIFQLFEMI*VPVNWSHVNKPPY

Parental  PKLGDNMKKLENCNYAVELGKNQAKFSLVGIAGQDLNEGNCTLTLALIWQLMRRYTLNILEEIGGGQKVN
          P.LG.NMKK.ENCN.AVELGKN.AKFSLVGIAGQDLNEGN.TLTLAL.WQLMR.YTLN.L...G.G.KVN
Retrocopy PALGGNMKKIENCNCAVELGKNEAKFSLVGIAGQDLNEGNSTLTLALVWQLMRQYTLNVLSDLGEGEKVN

Parental  DDIIVNWVNTTLKEAGKTSSISSFKDPKICTSLPVLDLIDAIRPGSINYDLL-TENLGDEEKLNNAKYAI
          D.II..WVN.T.K......SISSFKD..I.TSLPVLDL.DAI.P..........E.L.DE.KLNNAKYAI
Retrocopy DKIIIKWVNSTNKNI----SISSFKDKSISTSLPVLDLTDAIAPNAVRQEMVKREDLSDEDKLNNAKYAI

Parental  SMARKIGARVYALPEDLVEVNPKMVMTVFACLMGRGMKRV
          ..ARKIGAR.YALP.DLVEV.PKMVMTVF.CLM..G..R.
Retrocopy LVARKIGARIYALPDDLVEVKPKMVMTVFPCLMVKGLNRI

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_1057 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011426	1 retrocopy	retro_chof_203,
Choloepus hoffmanni	ENSCHOG00000012037	1 retrocopy	retro_chof_1057 ,
Mus musculus	ENSMUSG00000021998	2 retrocopies	retro_mmus_1307, retro_mmus_3697,