RetrogeneDB ID: retro_chof_1879

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_41317:2894..3403(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL12A
• Ensembl ID: ENSCHOG00000005206
• Aliases: None
• Description: myosin, light chain 12A, regulatory, non-sarcomeric [Source:HGNC Symbol;Acc:16701]

Sequence

>retro_chof_1879
AGCAAAAAGGCAAAAACCAAAACCACCAAGAAGCACCCTCAGTGCACAGCATCCAATGTGTTTGTCATGTTTGACCACTC
ACAGATTCAAGAGCTCAAAGATGCCTTCAACATGATCAATCAGAACAGAGATGGTTTCATCACCAAGGAAGATTTGCATG
ACATGCTTGCTTCTCTGGGAAAGAATCCAGCGGGTGCATACCTTGGGGCTATGATGAATGAGGCTCCAGGGACCATACAT
TTTACCATGTTCCTCACTATGTTTGCTAAGAAGTTAAATCGCACAGACCCAGAGGATGTCATCTGAAATGCTTTTGTGTG
CTTTGATGAAAAAGCAGCAGGCACCACTTAGGAGGATTACCTGAGAGAACTGCTAACAACTCTGGGGGATTGGTTTATAG
ATGAGGAAGTAGACGAGGTGTACAGAGAAGTGCAGATCAACAAAAGGAAACCTTCAACTGCATTGAGTTCACGTGCATCC
TTAAACACGGAGCGAGGGACAAGGATGAC

Alignment

ORF - retro_chof_1879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.19 %
• Parental protein coverage: 98.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKRAKTKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDEYLDA
          SK.AKTKTTKK.PQ...SNVF.MFD.SQIQE.K.AFNMI.QNRDGFI.KEDLHDMLASLGKNP...YL.A
Retrocopy SKKAKTKTTKKHPQCTASNVFVMFDHSQIQELKDAFNMINQNRDGFITKEDLHDMLASLGKNPAGAYLGA

Parental  MMNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATGTIQEDYLRELLTTMGDRFTDEEVDEL
          MMNEAPG.I.FTMFLTMF..KLN.TDPEDVI.NAF.CFDE.A.GT..EDYLRELLTT.GD.F.DEEVDE.
Retrocopy MMNEAPGTIHFTMFLTMFAKKLNRTDPEDVI*NAFVCFDEKAAGTT*EDYLRELLTTLGDWFIDEEVDEV

Parental  YREAPIDK-KGNFNYIEFTRILKHGAKDKDD
          YRE..I.K.K..FN.IEFT.ILKHGA.DKDD
Retrocopy YREVQINK<KETFNCIEFTCILKHGARDKDD

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_1879 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 10 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016024	2 retrocopies	retro_btau_1273, retro_btau_1693,
Canis familiaris	ENSCAFG00000029134	3 retrocopies	retro_cfam_166, retro_cfam_583, retro_cfam_79,
Choloepus hoffmanni	ENSCHOG00000005206	54 retrocopies	retro_chof_1002, retro_chof_1149, retro_chof_1238, retro_chof_1250, retro_chof_1273, retro_chof_1321, retro_chof_1326, retro_chof_135, retro_chof_1352, retro_chof_1363, retro_chof_1374, retro_chof_1439, retro_chof_1505, retro_chof_1520, retro_chof_1538, retro_chof_1553, retro_chof_1574, retro_chof_1594, retro_chof_1608, retro_chof_1641, retro_chof_1694, retro_chof_1783, retro_chof_1790, retro_chof_1798, retro_chof_1801, retro_chof_1804, retro_chof_1809, retro_chof_1875, retro_chof_1879 , retro_chof_1887, retro_chof_2059, retro_chof_2114, retro_chof_2157, retro_chof_2180, retro_chof_2353, retro_chof_2430, retro_chof_2492, retro_chof_2510, retro_chof_2516, retro_chof_2597, retro_chof_2638, retro_chof_2639, retro_chof_2689, retro_chof_543, retro_chof_545, retro_chof_584, retro_chof_606, retro_chof_618, retro_chof_667, retro_chof_686, retro_chof_696, retro_chof_729, retro_chof_752, retro_chof_949,
Callithrix jacchus	ENSCJAG00000038151	2 retrocopies	retro_cjac_1279, retro_cjac_3119,
Echinops telfairi	ENSETEG00000011271	3 retrocopies	retro_etel_393, retro_etel_439, retro_etel_96,
Microcebus murinus	ENSMICG00000017884	2 retrocopies	retro_mmur_1194, retro_mmur_1585,
Mus musculus	ENSMUSG00000024048	1 retrocopy	retro_mmus_1149,
Otolemur garnettii	ENSOGAG00000001340	7 retrocopies	retro_ogar_1877, retro_ogar_2516, retro_ogar_2536, retro_ogar_2540, retro_ogar_347, retro_ogar_517, retro_ogar_605,
Sorex araneus	ENSSARG00000011512	1 retrocopy	retro_sara_102,
Ictidomys tridecemlineatus	ENSSTOG00000027658	2 retrocopies	retro_itri_1480, retro_itri_896,