RetrogeneDB ID: retro_chof_1581

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_33088:1..634(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNOT7
• Ensembl ID: ENSCHOG00000000677
• Aliases: None
• Description: CCR4-NOT transcription complex, subunit 7 [Source:HGNC Symbol;Acc:14101]

Sequence

>retro_chof_1581
GTTGCAAGGCCCATTGGAGAATTCAGGAACAGTGCTGATTGTAGGTACCAACTCTTGCCATGTAATATAGACTTGTTAAG
ATAATTCAACTAGGACTGACATTTATGAATAAGCAAGGAGAATACCCTCCAAGAATTTCAACATGAAAGTTTAATTTTGA
ATTCAATTTGATGGAGGACATGTATGCTCAGAATGCTATAGAGCTACTAACAACATCTGATATCCAGTTTAAAAAACATG
AAGAAGAAGCAATTGAGAACTGGTACTTTGAAGAACTTCTTATGACATTGGAGTAATCATCCGTGAAAGGGTTAAATGAT
TATCCATTCATACTGGTTATGACTTTGGCTATTCAATCAAAATCCTGGCCAACTCTAACTTGCCTGCAGAAGAACTTGAC
CTCTTTGAGATATTCCCATTGTTTTTTCCTGTCATTTATGATGTGAAGTATCTTATGAAGAGCTGCAAAAATCTCAAAGG
TAGATTATAGGAAGTTTCTGAGAGTTAGAGCTGGAACAGATAGGATCACAATATCCATCAGGGTCTGATTCATTGCTTAC
AGGCATGGCCTTTTTGAAAATGAGAGACATGTTCTTTGAAGAGCACAGTGATGATGCCAAATACTGTGGCCAT

Alignment

ORF - retro_chof_1581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.74 %
• Parental protein coverage: 74.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VARPIGEFRSNADYQYQLLRCNVDLL-KIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIEL
          VARPIGEFR..AD..YQLL.CN.DLL.KIIQLGLTFMN.QGEYPP..ST..FNF.FNL.EDMYAQ..IEL
Retrocopy VARPIGEFRNSADCRYQLLPCNIDLL<KIIQLGLTFMNKQGEYPPRIST*KFNFEFNLMEDMYAQNAIEL

Parental  LTTSGIQFKKHEEEGIETQYFAELLMT-SGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEI
          LTTS.IQFKKHEEE.IE..YF.ELLMT..GV...E.VK.LS.H.GYDFGY.IKIL.NSNLP.EELD.FEI
Retrocopy LTTSDIQFKKHEEEAIENWYFEELLMT<IGVIIRERVK*LSIHTGYDFGYSIKILANSNLPAEELDLFEI

Parental  LRLFFPVIYDVKYLMKSCKNLKGGLQEVAE-QLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDA
          ..LFFPVIYDVKYLMKSCKNLKG.L.EV.E..LELE.IG.Q...GSDSLLTGMAF.KMR.MFFE.H.DDA
Retrocopy FPLFFPVIYDVKYLMKSCKNLKGRL*EVSE<ELELEQIGSQYPSGSDSLLTGMAFLKMRDMFFEEHSDDA

Parental  KYCGH
          KYCGH
Retrocopy KYCGH

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_1581 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 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000677	4 retrocopies	retro_chof_1431, retro_chof_1581 , retro_chof_822, retro_chof_963,
Callithrix jacchus	ENSCJAG00000011795	1 retrocopy	retro_cjac_720,
Felis catus	ENSFCAG00000000591	1 retrocopy	retro_fcat_1889,
Homo sapiens	ENSG00000198791	2 retrocopies	retro_hsap_211, retro_hsap_4851,
Gorilla gorilla	ENSGGOG00000015762	2 retrocopies	retro_ggor_282, retro_ggor_3027,
Macaca mulatta	ENSMMUG00000001873	1 retrocopy	retro_mmul_2592,
Monodelphis domestica	ENSMODG00000019055	2 retrocopies	retro_mdom_1898, retro_mdom_802,
Mustela putorius furo	ENSMPUG00000017972	1 retrocopy	retro_mputfur_1596,
Nomascus leucogenys	ENSNLEG00000002489	2 retrocopies	retro_nleu_1860, retro_nleu_2373,
Oryctolagus cuniculus	ENSOCUG00000014589	1 retrocopy	retro_ocun_118,
Otolemur garnettii	ENSOGAG00000006324	2 retrocopies	retro_ogar_1883, retro_ogar_505,
Pongo abelii	ENSPPYG00000018385	2 retrocopies	retro_pabe_3771, retro_pabe_428,
Sarcophilus harrisii	ENSSHAG00000011828	2 retrocopies	retro_shar_103, retro_shar_631,
Ictidomys tridecemlineatus	ENSSTOG00000009175	2 retrocopies	retro_itri_1729, retro_itri_1730,