RetrogeneDB ID: retro_chof_2287

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_6339:21775..23122(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1B2
• Ensembl ID: ENSCHOG00000003668
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2 [Source:HGNC Symbol;Acc:854]

Sequence

>retro_chof_2287
ATCAAGTTTCCTAGATATGCTGAGATTGTTCACTTGACATTACCAGATGGCACAAAAAGAAGTGGGCAGGTTCTAGAAGT
TAGTGGTTCCAAAGCAGTGGTTCAGGTATTTGAAGGGACTTCAGGTATAGATGCCAAGAAAACATCTTGTGAGTTTACAG
GGGATATTCTCCGAACACTAGTGTCTGAGGATATGCTTGGTCGGGTATTCAATGGATCTGGAAAACCCATTGACAGAGGC
CCTGTCGTGTTGGCCAAAGATTTCCTTGACATCATGGGCCAGCCAATCAATCCTCAGTGTCGAATCTACCCAGAAGAGAT
GATTCAGACTGGCATTTCAGCCATCGATGGCATGAACAGTATTGCTAGAGGGCAGAAAATTCCTATCTTCTCTGCTGCTG
GTTTACCACACAATGAGATTGCAGCTCAAATCTGTCGCCAGGCAGGTTTGGTAAAGAAATCCAAAGATGTTGTAGACTAC
AGCGAGGAAAATTTTGCAATTGTATTTGCTGCTATGGGTGTAAACATGGAAACTGCCCGATTCTTCAAGTCTGACTTTGA
AGAAAATGGCTCAATGGACAATGTCTGCCTCTTTCTGAACTTGGCTAATGACCCAACCATTGAGCGAATTATCACTCCTC
GTCTGGCTCTAACCACAGCTGAATTTCTGGCCTACCAATGTGAGAAACATGTGTTGGTTATCCTAACAGACATGAGTTCT
TATGCAGAAGCACTTCGAGAGGTTTCAGCAGCCAGGGAAGAAGTTCCTGGTCGATGAGGTTTCCCAGGTTATATGTATAC
AGATTTAGCCACAATATATGAACGCGCTGGTCGAGTGGAAGGTAGAAATGGCTCTATTACTCAAATGCCTATTCTCACCA
TGCCTAACGATGATATTACTCACCCTATCCCTGACTTGACTGGATATATTACAGAGGGTCAAATCTATGTGGACAGACAA
CTGCACAATAGACAGATTTACCCACCTATTAATGTGCTGCCTTCATTATCACAGTTAATGAAGTCTGCTATTGGAGAAGG
CATGACCAGAAAGGATCATGCCGATGTATCTAACCAGCTGTATGCGTGCTATGCAATTGGTAAGGATGTACAAGCCATGA
AAGCCGTAGTTAGAGAAGAAGCCCTTACCTCAGATGATCTTCTTTACTTGGAATTTCTCCAGAAGTTTGAAAGGAACTTT
ATTGCCCAGGGTCCTTATGAAAACCGCACTGTCTATGAGACTTTGGACATTGGCTGGCAACTGCTCCGAATCTTCCCCAA
AGAAATGCTGAAGAGAATCCCTCAGAGCACCCTGAGCGAGTTCTACCCTCGAGATTCTGCAAAGCAT

Alignment

ORF - retro_chof_2287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.0 %
• Parental protein coverage: 87.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKFPRYAEIVHLTLPDGTKRSGQVLEVSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTPVSEDMLGRVF
          .KFPRYAEIVHLTLPDGTKRSGQVLEVSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRT.VSEDMLGRVF
Retrocopy IKFPRYAEIVHLTLPDGTKRSGQVLEVSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTLVSEDMLGRVF

Parental  NGSGKPIDRGPVVLAEDFLDIMGQPINPQCRIYPEEMIQTGISAIDGMNSIARGQKIPIFSAAGLPHNEI
          NGSGKPIDRGPVVLA.DFLDIMGQPINPQCRIYPEEMIQTGISAIDGMNSIARGQKIPIFSAAGLPHNEI
Retrocopy NGSGKPIDRGPVVLAKDFLDIMGQPINPQCRIYPEEMIQTGISAIDGMNSIARGQKIPIFSAAGLPHNEI

Parental  A-QICRQAGLVKKSKDVVEYSEENFAIVFADMGVNMETARFFKSDFEENGSMDNVCLFLNLANDPTIERI
          A.QICRQAGLVKKSKDVV.YSEENFAIVFA.MGVNMETARFFKSDFEENGSMDNVCLFLNLANDPTIERI
Retrocopy AAQICRQAGLVKKSKDVVDYSEENFAIVFAAMGVNMETARFFKSDFEENGSMDNVCLFLNLANDPTIERI

Parental  ITPRLALTTAEFLAYQCEKHVLVILTDMSSYAEALREVSAAREEVPGRRGFPGYMYTDLATIYERAGRVE
          ITPRLALTTAEFLAYQCEKHVLVILTDMSSYAEALREVSAAREEVPGR.GFPGYMYTDLATIYERAGRVE
Retrocopy ITPRLALTTAEFLAYQCEKHVLVILTDMSSYAEALREVSAAREEVPGR*GFPGYMYTDLATIYERAGRVE

Parental  GRNGSITQMPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQIYPPINVLPSLSRLMKSAIGEGMTR
          GRNGSITQMPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQIYPPINVLPSLS.LMKSAIGEGMTR
Retrocopy GRNGSITQMPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQIYPPINVLPSLSQLMKSAIGEGMTR

Parental  KDHADVSNQLYACYAIGKDVQAMKAVVGEEALTSDDLLYLEFLQKFERNFIAQGPYENRTVYETLDIGWQ
          KDHADVSNQLYACYAIGKDVQAMKAVV.EEALTSDDLLYLEFLQKFERNFIAQGPYENRTVYETLDIGWQ
Retrocopy KDHADVSNQLYACYAIGKDVQAMKAVVREEALTSDDLLYLEFLQKFERNFIAQGPYENRTVYETLDIGWQ

Parental  LLRIFPKEMLKRIPQSTLSEFYPRDSAKH
          LLRIFPKEMLKRIPQSTLSEFYPRDSAKH
Retrocopy LLRIFPKEMLKRIPQSTLSEFYPRDSAKH

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_2287 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003668	1 retrocopy	retro_chof_2287 ,
Homo sapiens	ENSG00000147416	1 retrocopy	retro_hsap_4308,
Gorilla gorilla	ENSGGOG00000003888	1 retrocopy	retro_ggor_2879,
Microcebus murinus	ENSMICG00000001791	1 retrocopy	retro_mmur_854,
Nomascus leucogenys	ENSNLEG00000000794	1 retrocopy	retro_nleu_1460,
Pan troglodytes	ENSPTRG00000020040	1 retrocopy	retro_ptro_2917,
Tarsius syrichta	ENSTSYG00000010477	1 retrocopy	retro_tsyr_2096,
Tursiops truncatus	ENSTTRG00000013650	1 retrocopy	retro_ttru_1845,