RetrogeneDB ID: retro_chof_1028

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_186098:3642..4508(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANXA2
• Ensembl ID: ENSCHOG00000012143
• Aliases: None
• Description: annexin A2 [Source:HGNC Symbol;Acc:537]

Sequence

>retro_chof_1028
GTGGATGAGGTCACCATTGTCAACATCTTGACCAACCGCAGCAACGAGCAGAGACAGGATATTGCCTTCGCCTACCAGAG
AAGGACCAAAAAGGAACTCGCATCCTCATTGAAGTCAGCCTTATCCGGCCACCTGGAGGCGGTGATTTTGGGCCTGTTGA
AAACACCTGCTCAGTATGATGCTTCGGAGCTGAAAGCCTCCATGAAGGGTCTGGGGACAGATGAGGACTCCCTCATTGAG
ATCATCTGCTCAAGGACCAACCAGGAGCTGCAGGAAATCAACAGAGTCTACAAGGAGATGTACAAGACCGACCTGGAGAA
GGACATTATTTCCGACACATCTGGTGACTTCCGCAAATTGATGGTTGCCCTTGCAAAGGGTAGACGAGCAGAGGATGGCT
CTGTCATTGATTATGAACTGATTGACCAAGATGCCCGGGATCTCTACGATGCTGGAGTGAAGAGGAAAGGAACTGATGTC
CCCAAGTGGATCAGCATCATGACTGAGCGGAGCGTGTGCCACCTCCAGAAAGTATTTGAAAGGTACAAGAGCTATAGCCC
TTATGACATGTTGGAGAGCATCAAGAAGGAGGTCAAAGGTGACCTGGAAAATGCTTTCCTGAACCTGGTCCAGTGTATTC
AGAACAAGCCTCTGTATTCTGCTGATCGGCTGTACGACTCCATGAAGGGCAAGGGGACTGGTCACTAGGTCCTGATTAGG
ATCATGTCTCCCGCAGTGAAGTGGACATGTTGAAAATTAGGTCTGAATCCAAGAGAAAGTACGGCAAGTCCCTGTATTAC
TACATCCAGCCAGACACTGAGGGCAACCACCAGCAAGCACCGATGTACCTGTGTGGCGGAGACAAC

Alignment

ORF - retro_chof_1028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASSLKSALSGHLEAVILGLLKTPAQYDASELKASMKG
          VDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASSLKSALSGHLEAVILGLLKTPAQYDASELKASMKG
Retrocopy VDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASSLKSALSGHLEAVILGLLKTPAQYDASELKASMKG

Parental  LGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYEL
          LGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYEL
Retrocopy LGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYEL

Parental  IDQDARDLYDAGVKRKGTDVPKWISIMTERSVCHLQKVFERYKSYSPYDMLESIKKEVKGDLENAFLNLV
          IDQDARDLYDAGVKRKGTDVPKWISIMTERSVCHLQKVFERYKSYSPYDMLESIKKEVKGDLENAFLNLV
Retrocopy IDQDARDLYDAGVKRKGTDVPKWISIMTERSVCHLQKVFERYKSYSPYDMLESIKKEVKGDLENAFLNLV

Parental  QCIQNKPLYFADRLYDSMKGKGTRDKVLIRIM-VSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQK
          QCIQNKPLY.ADRLYDSMKGKGT...VLIRIM.VSRSEVDMLKIRSE.KRKYGKSLYYYIQ.DT.G..Q.
Retrocopy QCIQNKPLYSADRLYDSMKGKGTGH*VLIRIM<VSRSEVDMLKIRSESKRKYGKSLYYYIQPDTEGNHQQ

Parental  ALLYLCGGDD
          A..YLCGGD.
Retrocopy APMYLCGGDN

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_1028 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 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016686	3 retrocopies	retro_cfam_1631, retro_cfam_367, retro_cfam_707,
Choloepus hoffmanni	ENSCHOG00000012143	3 retrocopies	retro_chof_1028 , retro_chof_1965, retro_chof_815,
Felis catus	ENSFCAG00000007862	2 retrocopies	retro_fcat_594, retro_fcat_709,
Macropus eugenii	ENSMEUG00000008980	3 retrocopies	retro_meug_1000, retro_meug_312, retro_meug_389,
Myotis lucifugus	ENSMLUG00000002464	3 retrocopies	retro_mluc_1569, retro_mluc_2223, retro_mluc_2431,
Monodelphis domestica	ENSMODG00000011604	1 retrocopy	retro_mdom_1471,
Mustela putorius furo	ENSMPUG00000000762	2 retrocopies	retro_mputfur_73, retro_mputfur_79,
Pan troglodytes	ENSPTRG00000007132	2 retrocopies	retro_ptro_2106, retro_ptro_81,
Pteropus vampyrus	ENSPVAG00000011401	1 retrocopy	retro_pvam_389,