RetrogeneDB ID: retro_chof_2020

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_457123:1..616(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA1
• Ensembl ID: ENSCHOG00000000631
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 1 [Source:HGNC Symbol;Acc:5229]

Sequence

>retro_chof_2020
ATGGTCAAAGAAACCACTTGCTGTGACGTTTGGGGGGTCAAACCCAATGCCACACAGGAAGATTTGAAAAAGGCTTACAG
GAGACTAGCCTTTAAAAAAACACTCTGATAAGAATCCAAACCAAGGCAAGAAGTTTAAACAGATTTCTGAGGCTTATAAA
GTACTCCCTCATGAAAAGAAAAGAGAAGTATATGACAAAGGAGGAAAACAGACAATCAAAGAAGGTGGAGCAGGTGGGGG
TTTGACTCCCCCATGGACATCTTTGATATGTTTTTTTGGAGGTGGTAGAAGGATGCAGAGAGAAAGGAGAGGTAAAAATG
TTGTATATCAGCTCTCGCTAATCTTAGAAAATTTATATAATGGTGCAACAAGAAAACTAACTCTGCAAAAGAATACGACT
TGCGACAAATGTGAAGGCCGAGGTGGTAAGAAAGAGGCAGTAGAGTGCTATCCCAATTGCTGAAGGGCTGGAATGCAAAT
AAGAATCCATCCGATGGGACCGGGAATGGTTCCGCAAATTCAGTCTGTGTGCATGGAGTGTCAGGGCCATGGGGAATGGG
TCAGTTTTAAAGGTAGATGTAAAAGTTGCAGGGAAGGAAGATAGTTCAAGAGAAG

Alignment

ORF - retro_chof_2020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 51.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MVKETTYYDVLGVKPNATQEELKKAYRKLA-LKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKGGE
          MVKETT..DV.GVKPNATQE.LKKAYR.LA.LK.H.DKNPN.G.KFKQIS.AY.VL...KKRE.YDKGG.
Retrocopy MVKETTCCDVWGVKPNATQEDLKKAYRRLA>LKKHSDKNPNQGKKFKQISEAYKVLPHEKKREVYDKGGK

Parental  QAIKEGGAGGG-FGSPMDIFDMFF-GGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKC
          Q.IKEGGAGGG.F.SPMDIFDMFF.GGG.RMQRERRGKNVV.QLS..LE.LYNGATRKL.LQKN..CDKC
Retrocopy QTIKEGGAGGG<FDSPMDIFDMFF>GGGRRMQRERRGKNVVYQLSLILENLYNGATRKLTLQKNTTCDKC

Parental  EGRGGKKGAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSC-NGRKIVREK
          EGRGGKK.AVEC.PNC...GMQIRIH..GPGMV.QIQSVCMECQGHGE..S.K.RCKSC..GRKIV.EK
Retrocopy EGRGGKKEAVECYPNC*RAGMQIRIHPMGPGMVPQIQSVCMECQGHGEWVSFKGRCKSC<QGRKIVQEK

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_2020 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 85 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Choloepus hoffmanni	ENSCHOG00000000631	9 retrocopies	retro_chof_1760, retro_chof_186, retro_chof_2020 , retro_chof_2541, retro_chof_2694, retro_chof_287, retro_chof_417, retro_chof_498, retro_chof_946,
Callithrix jacchus	ENSCJAG00000008022	10 retrocopies	retro_cjac_1645, retro_cjac_1777, retro_cjac_2015, retro_cjac_2120, retro_cjac_2730, retro_cjac_2731, retro_cjac_2763, retro_cjac_3037, retro_cjac_3762, retro_cjac_887,
Cavia porcellus	ENSCPOG00000000462	6 retrocopies	retro_cpor_1456, retro_cpor_225, retro_cpor_386, retro_cpor_396, retro_cpor_561, retro_cpor_781,
Felis catus	ENSFCAG00000008729	5 retrocopies	retro_fcat_1241, retro_fcat_1407, retro_fcat_1502, retro_fcat_1984, retro_fcat_811,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Myotis lucifugus	ENSMLUG00000016086	7 retrocopies	retro_mluc_1245, retro_mluc_1485, retro_mluc_1737, retro_mluc_1878, retro_mluc_2062, retro_mluc_2579, retro_mluc_576,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Mustela putorius furo	ENSMPUG00000004231	2 retrocopies	retro_mputfur_1543, retro_mputfur_487,
Nomascus leucogenys	ENSNLEG00000005268	4 retrocopies	retro_nleu_1255, retro_nleu_2550, retro_nleu_2793, retro_nleu_509,
Oryctolagus cuniculus	ENSOCUG00000004833	2 retrocopies	retro_ocun_516, retro_ocun_70,
Rattus norvegicus	ENSRNOG00000007029	2 retrocopies	retro_rnor_2208, retro_rnor_608,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Ictidomys tridecemlineatus	ENSSTOG00000005200	4 retrocopies	retro_itri_265, retro_itri_303, retro_itri_378, retro_itri_809,