RetrogeneDB ID: retro_chof_549

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_12040:24061..25019(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIAS2
• Ensembl ID: ENSCHOG00000005911
• Aliases: None
• Description: protein inhibitor of activated STAT, 2 [Source:HGNC Symbol;Acc:17311]

Sequence

>retro_chof_549
GGCTGTGCAGCACCTCCTAAAATTGGGGTTGAAAAGAAGTGACCCAGATGCTCCGTGAATATTACATCCTTAGTTGGGTT
ATCTTCAGCTGTGCCAAATCAGATTTCCATTTCGTGGGCATCAGAAATTGGAAAGAATTACTCTGTATCTGTGTATCTTG
TATGTCTGTATATATGTATATCTTCAGCCATGTTATTACAGAGGTTAAAAATGAAAGGTATTAGAAACCCTGATCATTCT
AGAGTACTAACTAATGAAAAACATACTGCAGATCCTGATAGTGAAATTGCTACAACTAGCCTTCAGGTATCCTTGATGTG
TCCTTTAGGAAAAATGAGACTGACAATCCCATGCTGTACAGTGATTTGTATACACTTGCAGTGATTTGATGCTGCCCTTT
ATCTACAAATGAATGAGAAGCCCACCTGGATTTGTCCTATGTGTGACAAAAAGGCTGCCTATGAAAGTCTAATACTAGAT
GGGCTTTTAATTGAAATTCTCAATGACTGTCCTGATGTGGATGAGATCAAATTCCAAGATGGTGCATGGTGTCCAATGAG
ACTAAAGAAAGAAGCTATGAAAATATCCAGTCAACCGTGTACGAAAAGAGAAACTTTTAGAGTCTTCAGTAAACCTTGTT
AAGTGATGTAGACAATGAGGCAAACAAGAAGAAAGTGGATGTAATCGACCTAACAATAGAAAGCTCTTCTGATGAAAAGG
AAGACCCTCCTGCCAAAATGAAATGCATCTTTATGTCAGAAACACAAAGCAGCCCAACCAAAGGGGCTCTCATGTATAGC
CCTCTTCTGTAAGGGTGCCCCAGGTGACTTCGGTTGATCCTGCTACTGTTCCGCCTTCATTAACAGGCTACTCATTACCA
TTCCACCACGCACCCATATCAAGCATGTCATCGGATTCGCCAGGTTTGCATTTTCTTTCCCTTATTCCAGTTGATCCC

Alignment

ORF - retro_chof_549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.86 %
• Parental protein coverage: 51.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GYAPPPKNGIEQKRPGRPLNITSLVRLSSAVPNQISISWASEIGKNYSMSVY---LVRQLTSAMLLQRLK
          G.A.PPK.G.E.K.P....NITSLV.LSSAVPNQISISWASEIGKNYS.SVY...L.....SAMLLQRLK
Retrocopy GCAAPPKIGVEKK*PRCSVNITSLVGLSSAVPNQISISWASEIGKNYSVSVYLVCLYICISSAMLLQRLK

Parental  MKGIRNPDHSRALIKEKLTADPDSEIATTSLRVSLMCPLGKMRLTIPCRAVTCTHLQCFDAALYLQMNEK
          MKGIRNPDHSR.L..EK.TADPDSEIATTSL.VSLMCPLGKMRLTIPC..V.C.HLQ.FDAALYLQMNE.
Retrocopy MKGIRNPDHSRVLTNEKHTADPDSEIATTSLQVSLMCPLGKMRLTIPCCTVICIHLQ*FDAALYLQMNE-

Parental  KPTWICPVCDKKAAYESLILDGLFMEILNDCSDVDEIKFQEDGSWCPMRPKKEAMKVSSQPCTKIETSSV
          KPTWICP.CDKKAAYESLILDGL..EILNDC.DVDEIKFQ.DG.WCPMR.KKEAMK.SSQPCTK.ET..V
Retrocopy KPTWICPMCDKKAAYESLILDGLLIEILNDCPDVDEIKFQ-DGAWCPMRLKKEAMKISSQPCTKRETFRV

Parental  LSKPCSV-TVANEANKKKVDVIDLTIESSSDEEEDPPAKRKCIFMSETQSSPTKGVLMYQ-PSSVRVPSV
          .SKPC.V..V.NEANKKKVDVIDLTIESSSDE.EDPPAK.KCIFMSETQSSPTKG.LMY..PSSVRVP.V
Retrocopy FSKPC*V<DVDNEANKKKVDVIDLTIESSSDEKEDPPAKMKCIFMSETQSSPTKGALMYS<PSSVRVPQV

Parental  TSVDPAAIPPSLTDYSVPFHHTPISSMSSDLPG-DFLS-IPVDP
          TSVDPA..PPSLT.YS.PFHH.PISSMSSD.PG..FLS.IPVDP
Retrocopy TSVDPATVPPSLTGYSLPFHHAPISSMSSDSPGLHFLSLIPVDP

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_549 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005911	1 retrocopy	retro_chof_549 ,
Callithrix jacchus	ENSCJAG00000008117	1 retrocopy	retro_cjac_4167,
Gallus gallus	ENSGALG00000001843	1 retrocopy	retro_ggal_24,