RetrogeneDB ID: retro_chof_2198

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_57825:4192..5055(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT2
• Ensembl ID: ENSCHOG00000008715
• Aliases: None
• Description: septin 2 [Source:HGNC Symbol;Acc:7729]

Sequence

>retro_chof_2198
GAGAAAACTGAAAGAACTGTCCGAATTGAGGCTTCAACGGTTGAGACTGAAGAGCGAGGAGTCAAGCTGCGCCTGACTGT
GGTGCACTCGCCCGGCTACCGTGACGCCATCAACTGCAGAGACTGTTTTAAGACCATCGTCTCCTGCACTGAGGAGCAGT
TTGAACGGTACCCGCACGACAAGAGTGGGCTGAATCGACGGCACATCACAGATAATCGAGTGCACTGCTGCTTTTACTTC
ATTTCACCTTTGGACGTGGACTTAAGCACTTGGACGCGGCGTTCATGAAGGCGATCCACAACACGGTCAGCATCGCGCCC
GTCATCGCCAAGGCCGACACGCTGACTCTGAAGGAGTGGGAGCAGCTGAAGAGGATTCTGGATGAAACCGAAGAACATAG
CATCAAAATCTATCACTTACCTGATGCAGAATCAGATGAAGAGGAGGATGTTAAAGAGCAGACGTGACTTCTCAAGGAGA
GCATTCCGCTTTCCGTGGTTGGATCCAGTCAGTTTATTGAAGCCGAAGGCAAGAAGGTTGGAGGCCGCCTCTACCCATGG
GGCGTCGTGGAGGTGGCAAATCCGGGGCACAACGACTTCCCGAAGCTGAGGACAGTGCTCATCACCCACGTGCAGGACCT
GCAGGAGGTGACCCAGGACCTGCGCCGCGGAAACTTCCGTTCCGAGCGGCTCAAGTGGAGCGGCAGGAAAGTGGAGAATG
AGGATATGAACAAAGACCAGATCTTGCTGTAAAAGGAAGCCGAACTTCGTCACATGCAAGAGATGATTGCAAGAATGCAG
GAGCAGATGCAGATGCAGATGCAAGGGGGAGACAGTGATGGCAGTGCTCACGGGCCCCACGTG

Alignment

ORF - retro_chof_2198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.34 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKIERTVQIEASTVEIEERGVKLRLTVVDTPGYGDAINCRDCFKTIISYIDEQFERYLHDESGLNRRHII
          EK.ERTV.IEASTVE.EERGVKLRLTVV..PGY.DAINCRDCFKTI.S...EQFERY.HD.SGLNRRHI.
Retrocopy EKTERTVRIEASTVETEERGVKLRLTVVHSPGYRDAINCRDCFKTIVSCTEEQFERYPHDKSGLNRRHIT

Parental  DNRVHCCFYFISP-FGHGLKPLDVAFMKAIHNKVNIVPVIAKADTLTLKERERLKRRILDEIEEHSIKIY
          DNRVHCCFYFISP.FG.GLK.LD.AFMKAIHN.V.I.PVIAKADTLTLKE.E.LK.RILDE.EEHSIKIY
Retrocopy DNRVHCCFYFISP<FGRGLKHLDAAFMKAIHNTVSIAPVIAKADTLTLKEWEQLK-RILDETEEHSIKIY

Parental  HLPDAESDEDEDFKEQTRLLKASIPFSVVGSNQLIEAKGKKVRGRLYPWGVVEVENPEHNDFLKLRTMLI
          HLPDAESDE.ED.KEQT.LLK.SIP.SVVGS.Q.IEA.GKKV.GRLYPWGVVEV.NP.HNDF.KLRT.LI
Retrocopy HLPDAESDEEEDVKEQT*LLKESIPLSVVGSSQFIEAEGKKVGGRLYPWGVVEVANPGHNDFPKLRTVLI

Parental  THMQ-LQEVTQDLHYENFRSERLK-GGRKVENEDMNKDQILLEKEAELRRMQEMIARMQAQMQMQMQGGD
          TH.Q.LQEVTQDL...NFRSERLK..GRKVENEDMNKDQILL.KEAELR.MQEMIAR..........GGD
Retrocopy THVQDLQEVTQDLRRGNFRSERLKWSGRKVENEDMNKDQILL*KEAELRHMQEMIARXXXXXXXXXXGGD

Parental  GDGSAHGPHV
          .DGSAHGPHV
Retrocopy SDGSAHGPHV

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_2198 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 18 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002608	1 retrocopy	retro_btau_1185,
Canis familiaris	ENSCAFG00000012960	1 retrocopy	retro_cfam_1477,
Choloepus hoffmanni	ENSCHOG00000003906	1 retrocopy	retro_chof_1543,
Choloepus hoffmanni	ENSCHOG00000008715	5 retrocopies	retro_chof_1371, retro_chof_1579, retro_chof_2198 , retro_chof_275, retro_chof_614,
Choloepus hoffmanni	ENSCHOG00000009949	1 retrocopy	retro_chof_2159,
Callithrix jacchus	ENSCJAG00000006122	1 retrocopy	retro_cjac_1501,
Cavia porcellus	ENSCPOG00000013687	1 retrocopy	retro_cpor_845,
Loxodonta africana	ENSLAFG00000011964	1 retrocopy	retro_lafr_4,
Macropus eugenii	ENSMEUG00000016519	1 retrocopy	retro_meug_39,
Myotis lucifugus	ENSMLUG00000007108	1 retrocopy	retro_mluc_1594,
Monodelphis domestica	ENSMODG00000016041	1 retrocopy	retro_mdom_888,
Mustela putorius furo	ENSMPUG00000000166	1 retrocopy	retro_mputfur_436,
Nomascus leucogenys	ENSNLEG00000013873	1 retrocopy	retro_nleu_1848,
Otolemur garnettii	ENSOGAG00000004457	1 retrocopy	retro_ogar_2239,
Pteropus vampyrus	ENSPVAG00000000558	1 retrocopy	retro_pvam_448,
Rattus norvegicus	ENSRNOG00000017952	1 retrocopy	retro_rnor_1110,
Ictidomys tridecemlineatus	ENSSTOG00000013357	1 retrocopy	retro_itri_1227,
Drosophila melanogaster	FBgn0011710	1 retrocopy	retro_dmel_35,