RetrogeneDB ID: retro_chof_579

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_123480:4712..5950(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLRG1
• Ensembl ID: ENSCHOG00000001013
• Aliases: None
• Description: pleiotropic regulator 1 [Source:HGNC Symbol;Acc:9089]

Sequence

>retro_chof_579
ATGGTCGAGGAGGGGCAGAAACATTCTGTGCACTCACTTGTGTTTAGGTCATTGAAGAGGACACATGACATGTTTGTAGC
AAATATTGGGAAACCTGTGCCTTTGGATGAAGAAAATCATAAACGAAAAATGTCAATCAAGCTTTGTAATGAATATGATC
CTGTGTTGCATACGCCTACTTTGAAAGAAAATTTTAAAGAGGTGGGCCCTCAGTGCAGCAGATTCATATGTTTCATAAAC
AATATCCTGCCAATCAAAGACAAGAGGTTGAATATTCGGCGATGGGTGCACTTCAGTATCCACCAGGGCCTGGGGTTGCT
TTGACAGTGGATACTAAAATCCAAAGGATGCCGAGTGGATCAGCTGTATAGTCCTTAGCTGTGGCATTACCTTCTTCTCA
GGCCAGTGCTGATGCAAATAGTATTGTACCTGGTGGAAGTGAATACTGCCATCCTGGGGCTTCTGATCTTTCACAGCCTG
CAGTGATGACTTCAGTTATTATGGAGAACTCTGCACTGATGGCCAAAAAAGCCCCCACAATGCCAATACCCCAATGGCAC
CCACCTTGAAAACTCTACAGGGTTATTAGTGGGTATCTTGGCTGGGTTCATTGTATTGCTTGTGGAACCTGGAAATCAGT
GGTTTATTACTAGTTATGCTGAAAGAACTATAAAGATCTAGGACTTTGCTAGTTGCAAATTAAAACTGTCATGGACTGGG
CACATTAGTACAGTGCATGGGGTAATAGTGAGCACGAGGAGCCCATATCCATTCTCTTGTGGAGAAGACAAACAAGTAAA
ATGCTGGGATCGTAATATAATGAGGTTATAAGGCACTGTCATGGACATCTAAGTGCAGTGTATGGTTTGGATTTGCACCC
AACAATTGATGCGCTGGTAACCTGTAGTCAAGATTCAATTGCACGGTTTTGGGATGTGAGAACTAAAGTCAGTGTACACT
TATTATCTGGACATACAAATGCAGTTGCTACAGTGAGGTGTCAAGCTGCAGAACCACAAATTATTACTGGAAGCCATGTC
ACTACATTATGATTATAGGATTTGGTGGCTGGAAAAATAAGAGTCACATTAACAAATCACAAAAAGTCAGTGAGGGCTGT
GATTTTACATCCAAGACATTACACGTTTGCATCTGGTTCTCTAGATAACATAAAACAGTGGAAATTCCCTGATGGAAGTT
TCATTCAAAATCTTTCTGGTCACAATGCTATTATTAAT

Alignment

ORF - retro_chof_579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.57 %
• Parental protein coverage: 80.78 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MICEVQKHSVHTLVFRSLKRTHDMFVADNGKPVPLDEESHKRKMAIKLHNEYGPVLHMPTLKENFKEK-G
          M..E.QKHSVH.LVFRSLKRTHDMFVA..GKPVPLDEE.HKRKM.IKL.NEY.PVLH.PTLKENFKE..G
Retrocopy MVEEGQKHSVHSLVFRSLKRTHDMFVANIGKPVPLDEENHKRKMSIKLCNEYDPVLHTPTLKENFKEV<G

Parental  PP-SAADSYG-HKQYPANQGQEVEYLVTGTHPYPPGPGVALTADTKIQRMPSESAAQSLAVALPSSQARV
          P..SAADSY..HKQYPANQ.QEVEY...G...YPPGPGVALT.DTKIQRMPS.SA..SLAVALPSSQA..
Retrocopy PS<SAADSYV>HKQYPANQRQEVEYSAMGALQYPPGPGVALTVDTKIQRMPSGSAV*SLAVALPSSQASA

Parental  DANRTVPGGNEYRHPGASDRSQPAVMTSVIMETGNTKNSALMAKKPTMPKPQW-PPWKLYRVISGHLGWV
          DAN..VPGG.EY.HPGASD.SQPAVMTSVIME...........K.PTMP.PQW.PP.KLYRVISG.LGWV
Retrocopy DANSIVPGGSEYCHPGASDLSQPAVMTSVIME----NSALMAKKAPTMPIPQWHPP*KLYRVISGYLGWV

Parental  RCIA-VEPGNQWFVTGSADRTIKIWDLASGKLKLSLTGHISTVRGVIVSARSPYLFSCGEDKQVKCWDLE
          .CIA.VEPGNQWF.T..A.RTIKI.D.AS.KLKLS.TGHISTV.GVIVS.RSPY.FSCGEDKQVKCWD..
Retrocopy HCIA>VEPGNQWFITSYAERTIKI*DFASCKLKLSWTGHISTVHGVIVSTRSPYPFSCGEDKQVKCWDRN

Parental  -YNKVIRHYHGHLSAVYGLDLHPTIDVLVTCSRDSTARIWDVRTKASVHTLSGHTNAVATVRCQAAEPQI
          .YN.VIRH.HGHLSAVYGLDLHPTID.LVTCS.DS.AR.WDVRTK.SVH.LSGHTNAVATVRCQAAEPQI
Retrocopy <YNEVIRHCHGHLSAVYGLDLHPTIDALVTCSQDSIARFWDVRTKVSVHLLSGHTNAVATVRCQAAEPQI

Parental  ITGSHDTTIRLWDLVAGKTRVTLTNHKKSVRAVVLHPRHYTFASGSPDNIKQWKFPDGSFIQNLSGHNAI
          ITGSH.TT..L.DLVAGK.RVTLTNHKKSVRAV.LHPRHYTFASGS.DNIKQWKFPDGSFIQNLSGHNAI
Retrocopy ITGSHVTTL*L*DLVAGKIRVTLTNHKKSVRAVILHPRHYTFASGSLDNIKQWKFPDGSFIQNLSGHNAI

Parental  IN
          IN
Retrocopy IN

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_579 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	ENSCHOG00000001013	1 retrocopy	retro_chof_579 ,
Myotis lucifugus	ENSMLUG00000008318	1 retrocopy	retro_mluc_812,
Ornithorhynchus anatinus	ENSOANG00000005295	1 retrocopy	retro_oana_80,