RetrogeneDB ID: retro_chof_1909

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_420816:109..973(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTA2
• Ensembl ID: ENSCHOG00000000759
• Aliases: None
• Description: actin, alpha 2, smooth muscle, aorta [Source:HGNC Symbol;Acc:130]

Sequence

>retro_chof_1909
CACCCCATTAAGCAAGGCATCAACTGGGACGACATGGAGAAGATGAAGAAAATCTGGCACCATACCTACAACGAGCTGCG
CATGTCGCCCGAGGAGCACCCCGTGCTGCTGACGGAGGCGCCCCTGAACCCCAAGGCCAATAGGGAGAAGATGACGCAGA
TCATGTTCGAGACTTTCAACATGCCCGCCATGTACGTGGCCATCCAGGCCGTGCTGTCGCTGTATGCGTCGGGCGCACCA
CGGGCATCGTGATGGACTCGGGCCACGGCGTCACGCACACGGTGCCCATCTACAAGGGCTACGCGCTGCTGCATGCCATC
CTGCGCCTGGACCTGGCGGGCTGTCATCTGACAGACTACCTGTTGAGGATACTCATGGAGCATGGCTACAGTTTCACCAC
CATGGGTGAGAGGGATATTGTGTGTGACATTAAAGAACACCTCTGTTTCATTGCCTTGGACTTCAAGCAGGAGATGGCCA
CCACTGCCTTGTCCACCTCCCTGGATAAGAGCTATAAGCTTCCTGATGGGAAGTTCATCTCCATTGGCAGTGATCAGTTC
TGCTGTCATGAAGCCCTCTTCCAGCCTTCCTTCCTGGGCATGGAATCCTATGGCATCCATGAAATTGCCTTCAACTCCAT
AATAAAATGTGTTGTGACCATCCACAAGAATCTCTATGCCAATGTGGTGCTGTCTGGTGGGACCACTATGTATCTGAGCA
TTACTGACAGAATGCAGAAGGAGATCACAGTGCTTTGCACCCAGCACAATGAAGACAAAGGCCATTGCCCCCTTTGAGCA
CAAGTACTCTGTGTGGATTGTTGGATCCATACTGGCCTCACTGTCCACATTCTAGCAGATGTGG

Alignment

ORF - retro_chof_1909 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.74 %
• Parental protein coverage: 76.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YPIEHGIITNWDDME---KIWHHSFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVA
          .PI..GI..NWDDME...KIWHH..YNELR..PEEHP.LLTEAPLNPKANREKMTQIMFETFN.PAMYVA
Retrocopy HPIKQGI--NWDDMEKMKKIWHHT-YNELRMSPEEHPVLLTEAPLNPKANREKMTQIMFETFNMPAMYVA

Parental  IQAVLSLYASG-RTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTA
          IQAVLSLYASG.RTTGIV.DSG.GVTH.VPIY.GYAL.HAI.RLDLAG..LTDYL..IL.E.GYSF.T..
Retrocopy IQAVLSLYASG<RTTGIVMDSGHGVTHTVPIYKGYALLHAILRLDLAGCHLTDYLLRILMEHGYSFTTMG

Parental  EREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGI
          ER.IV.DIKE.LC..ALDF..EMAT.A.S.SL.KSY.LPDG..I.IG...F.C.E.LFQPSF.GMES.GI
Retrocopy ERDIVCDIKEHLCFIALDFKQEMATTALSTSLDKSYKLPDGKFISIGSDQFCCHEALFQPSFLGMESYGI

Parental  HETTYNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITAL-APSTMKIKIIAPPERKYSVWIGG
          HE...NSI.KC...I.K.LYAN.VLSGGTTMY..I.DRMQKEIT.L.APSTMK.K.IAP.E.KYSVWI.G
Retrocopy HEIAFNSIIKCVVTIHKNLYANVVLSGGTTMYLSITDRMQKEITVL>APSTMKTKAIAPFEHKYSVWIVG

Parental  SILASLSTFQQMW
          SILASLSTF.QMW
Retrocopy SILASLSTF*QMW

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_1909 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 12 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000759	3 retrocopies	retro_chof_1909 , retro_chof_2042, retro_chof_21,
Dasypus novemcinctus	ENSDNOG00000006719	1 retrocopy	retro_dnov_32,
Echinops telfairi	ENSETEG00000008526	1 retrocopy	retro_etel_41,
Macropus eugenii	ENSMEUG00000010843	1 retrocopy	retro_meug_1374,
Myotis lucifugus	ENSMLUG00000015509	3 retrocopies	retro_mluc_190, retro_mluc_427, retro_mluc_90,
Nomascus leucogenys	ENSNLEG00000012233	1 retrocopy	retro_nleu_2313,
Oryctolagus cuniculus	ENSOCUG00000008193	3 retrocopies	retro_ocun_1306, retro_ocun_1421, retro_ocun_919,
Pongo abelii	ENSPPYG00000002459	1 retrocopy	retro_pabe_3027,
Sorex araneus	ENSSARG00000005778	1 retrocopy	retro_sara_732,
Tupaia belangeri	ENSTBEG00000017616	3 retrocopies	retro_tbel_1555, retro_tbel_3014, retro_tbel_4616,
Tarsius syrichta	ENSTSYG00000008155	5 retrocopies	retro_tsyr_1282, retro_tsyr_2102, retro_tsyr_858, retro_tsyr_9, retro_tsyr_92,
Vicugna pacos	ENSVPAG00000010621	3 retrocopies	retro_vpac_12, retro_vpac_355, retro_vpac_651,