RetrogeneDB ID: retro_chof_2578

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_87474:5..1612(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000013540
• Aliases: None
• Description: None

Sequence

>retro_chof_2578
AATATCCATTCCATTACTACAGGGAACAGTCCACCCCATGAGCGATTGCTTATGAGTGATGGATTGAACAATCTATCCTC
TTTCATGTTGGCAACACAGTTGAACCCTCTTGTTGAGAACGAACAATTGTCCAGCCACTGTATTAGCCAGATTAACTGAT
TTATTGTTAACACTCTGAAAGTTGAAAGGAGAGTAGTTATTTTGATGGAACTAGAAGTTTTGAAATCAGCTGAAGCAGTT
GGATTAAAGATTGGCAATCCAGTATCCTATAATGAAGGACAGCAAGTTGTTCCTACTCCTGTCTCAGCAACCAATCCACC
AACCAGCAAGCCCCAGCAACAGAATGGAAGTTCAGGAACGGGTTCCACCGTATCTAAGTCTTTTGGTGTCTCAAAGACAT
TTGGAAAAACTGGAAATACCAGCCTCGTGAACATTTCTGGGGGAACACAGTCCAAAGTGGTACCCATTGCCAGCCTTACC
CCTTACCAGTACAAGTGGACTATTTGTGCTCGAGTTACCAATAAAAATCAGATCCATACCTAGAGCAATTCCCGAGGGGA
AGGAAAGCTTTTCTCTTTAGAACTGGTTGATGAAAGTGGTGAAATCAGAGTTACTGCTTTCAACAGGCAAGTGGACAAGT
TCTTTCCCCTTATTGAAGTGAACAAGGTTTATTACTTCTCAAAAGGCACCTAAAGATTGCTAACAAGCAATTCACAGCTG
TTAAAAATGACCATGAGATGACTTTCAATAATGAGACATCTGTCATGCCCTGTGAAGATGGTCATCATTTATCTACAGTT
CACTTTGATTTCACTGGGATTGGTGACCTAGAGAACAAGTCTAAAGACTCACTTGTAGACATAATTGGAATCTGCAAGAG
TTATGAAGATGCCACTAAAATCACAGTGAAATCTAATAACAGAGAAGTTTCTAAGAGAAATATCTACTTGATGGACATGT
CAGGGAAGGTGGTGACTGCTACTCTGTGGGGAGAAGATGCTGATAGATTTGATGGGTCTAGACATTCCTTGATGGCTATC
AAAGGAGCCAGAGTTTCTGATTTTGGTGGACGGAGCCTCTCTGTACTGTCTTCAAGCACTGTCATTGTGAATCCTGACAT
CCCCGATAGATGATGGGAGAGGTGATGGTTTGACTCAGAAGGACAAGCCTTAGATGGTGTTTCCATCTCTGATCTAAAGA
GTGGAGGAGTAGGAGGGTGCAACACCAACTGGAAAACCCTATATGAGGTTAAATCAGAGAATCTGGATCAAGGTGACAAG
GCGGACTATTTCAGCTGTGTGGCAACAGTGGTGTATCTCCTCAAGGAGAATTGTATGTACCAGGCCTGCCCAACTCAGGA
CTGCAACAAGAAAGTGATTGATCAGCAGAATGGATTATACCGCTGTGAGAAGTGTGACAGTGAATTTCCCAATTTCAAGT
ACTGCTTGAACCTATCAGTAAATATTGCAGATTTTCAAGAGAATCAGTGGGTGACTCCTTTCCAGGAGTCTGCAGAGGCT
ATCCTCGGACAAAGTGCTGCTTATCTGGGGGAATTAAAAGAGAAGAATGAGCAGGCATTTGAGGAAGTTTCCCAGAATGC
CAACTTC

Alignment

ORF - retro_chof_2578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 91.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVENEQLSSHXXXXXXXXXXXXXXXXXRVVILME
          NI..ITTGNSPP..RLLMSDGLN.LSSFMLATQLNPLVENEQLSSH.................RVVILME
Retrocopy NIHSITTGNSPPHERLLMSDGLNNLSSFMLATQLNPLVENEQLSSHCISQIN*FIVNTLKVERRVVILME

Parental  LEVLKSAEAVGLKIGNPVPYNEGHGQQQVVPTPVSATSPPTSKPQQQNGSSGMGSTVSKSFGVSKTFGKA
          LEVLKSAEAVGLKIGNPV.YNEG...QQVVPTPVSAT.PPTSKPQQQNGSSG.GSTVSKSFGVSKTFGK.
Retrocopy LEVLKSAEAVGLKIGNPVSYNEG---QQVVPTPVSATNPPTSKPQQQNGSSGTGSTVSKSFGVSKTFGKT

Parental  GNTNLMNSPGGTQSKVVPIASLTPYQSKWTICARVTNKSQIRTWSNSRGEGKLFSLELVDESGEIRVTAF
          GNT.L.N..GGTQSKVVPIASLTPYQ.KWTICARVTNK.QI.T.SNSRGEGKLFSLELVDESGEIRVTAF
Retrocopy GNTSLVNISGGTQSKVVPIASLTPYQYKWTICARVTNKNQIHT*SNSRGEGKLFSLELVDESGEIRVTAF

Parental  NEQVDKFFPLIEVNKVYYFSKGT-LKIANKQFTAVKNDYEMTFNNETSVMPCEDGHHLPTVHFDFTGIGE
          N.QVDKFFPLIEVNKVYYFSKGT.LKIANKQFTAVKND.EMTFNNETSVMPCEDGHHL.TVHFDFTGIG.
Retrocopy NRQVDKFFPLIEVNKVYYFSKGT<LKIANKQFTAVKNDHEMTFNNETSVMPCEDGHHLSTVHFDFTGIGD

Parental  LENKSKDSLVDIIGICKNYEDATKITVKSNNREVSKRDIYLMDMSGKVVTATLWGEDADRFDGSRQPVMA
          LENKSKDSLVDIIGICK.YEDATKITVKSNNREVSKR.IYLMDMSGKVVTATLWGEDADRFDGSR...MA
Retrocopy LENKSKDSLVDIIGICKSYEDATKITVKSNNREVSKRNIYLMDMSGKVVTATLWGEDADRFDGSRHSLMA

Parental  IKGARVSDFGGRSLSVLSSSTVIVNPDIPEAYKLRGWFDSEGQALDGVSISDLKSGGVGGGNTNWKTLYE
          IKGARVSDFGGRSLSVLSSSTVIVNPDIP.....R.WFDSEGQALDGVSISDLKSGGVGG.NTNWKTLYE
Retrocopy IKGARVSDFGGRSLSVLSSSTVIVNPDIPDR*WER*WFDSEGQALDGVSISDLKSGGVGGCNTNWKTLYE

Parental  VKSENLGQGDKADYFSCVATVVYLRKENCMYQACPTQDCNKKVIDQQNGLYRCEKCDSEFPNFKYRMILS
          VKSENL.QGDKADYFSCVATVVYL.KENCMYQACPTQDCNKKVIDQQNGLYRCEKCDSEFPNFKY...LS
Retrocopy VKSENLDQGDKADYFSCVATVVYLLKENCMYQACPTQDCNKKVIDQQNGLYRCEKCDSEFPNFKYCLNLS

Parental  VNIADFQENQWVTSFQESAEAILGQSAAYLGELKEKNEQAFEEVFQNANF
          VNIADFQENQWVT.FQESAEAILGQSAAYLGELKEKNEQAFEEV.QNANF
Retrocopy VNIADFQENQWVTPFQESAEAILGQSAAYLGELKEKNEQAFEEVSQNANF

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_2578 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013540	2 retrocopies	retro_chof_167, retro_chof_2578 ,
Rattus norvegicus	ENSRNOG00000003123	1 retrocopy	retro_rnor_1373,
Ictidomys tridecemlineatus	ENSSTOG00000022475	1 retrocopy	retro_itri_677,