RetrogeneDB ID: retro_chof_2670

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_95790:2262..3745(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALDH6A1
• Ensembl ID: ENSCHOG00000002670
• Aliases: None
• Description: aldehyde dehydrogenase 6 family, member A1 [Source:HGNC Symbol;Acc:7179]

Sequence

>retro_chof_2670
AAACTCTTCATTAATGGGAAATTTGTTGAATCCAAAAGTGACAAATGGATTGAGAGCCACAACCCAGCCACCAATGAAGT
AATTGGTTGGGTCCCTCAGGCTACTAGGGCTGAAATGGATGCAGCTGTTGCTTTCTGCAAATGTGCTTTTCCCACACGGG
CAGACACTTCAGTTTTAAGCCTTCAGCATCTCCTGCTCCACTATCAACAACTTATTAAAGAAAACTTGAAAGAAATCGCC
AGGTTAATCACATTGGAACAAGGAAAGACCCTAGCTGATGCCGAAGGAGATGTATTTCGAGGCCTTCAGGTGGTTGAGCA
TGCCTGTAGTGTGACAGCCCTCATGATGGGAGAGACCATGCCATCCATCACCAAAGACATGGACCTTTATTCCTACCGTC
TTCCCCTGGGTGTGTGTGCAGGCATTGCACCATTCAATTTTCCTGCCATGATCCCCCTTTGGATGTTTCCCATGGCCATG
GTGTGTGGAAATACCTTCCTAATGAAACCATCAGAGTGAGTCCCTGGAGCAACTATGCTTCCAGCTAAGTTGCTCCAAGA
CTCTGGTGCTCCAGATGGAACACTGAACATCATCCATCGACAACATGAAGCTGTAAATTTTATTTGTGATCATCCGGCCA
TCAAAGCAATCAGCTTTGTGGGATCCAACTAGACAGGAGAGTACATCTTCGAGAAAGGGTCAAGACATGGCAAGAGAGTT
CAAGCCAATATGGGAGCCAAGAACCATGGAGTGGTCATGCCAGATGCCAATAAGGAAAATATCCTGAACCAGCTAGTTGG
GGCAGCATTTGGAGCAGCTGGTCAGCGCTGCATGGCTCTTTCAACAGCGATTCTTGTGGGAGATGCCAAGAAATGGCTGC
CAGAGCTGGTGGAGCGCACCAAAAACCTGAGAGTCAATGCAGGAGACCAGCCGGGAGCCAATTTTGGCCCTCTGATAACT
CCCCAGGCTAAAGAGTGAGTCTGTAATCTGACTGATAGTGGAACAAAGGAGGGAGCGTCCATCCTCTTTGATGGACAAAA
AAATTAATGTCAAAGGTTATGAAAATGGCAACTTTGTTGGACCCACCATCATCTCAGATGTCAAGCCAAATATGACCTGT
TACAAAGAAGAGATTTTTGGTCCAGTTCTTGTGGTTCTGGAGACAGAGACATTGGATGCAGCCATCAAGATTGTAAATGA
CAACCCATACGGAAATGGAACTGCCATCTTCACCACCAATGGACCCACAGCTCGAAAATATTCACACCTAGTGGATGTCG
GACAGGTGGGTGTCAATGTACCCATTCCAGTGCCTTTGCCAATGTTCTCATTCACTGGCTCACGATCTTCCTTCAGGGGA
GACACCAATTTCTATGGCAAACAGGGCTTCCAATTCTACACTCAGTTAAAGACCATCACTTCTCAGTGGAAAGAAGATGC
TACTCTTTCTTCACCTGTTGTAGTCATGCCTACAATGGGCCAT

Alignment

ORF - retro_chof_2670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.31 %
• Parental protein coverage: 95.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLFIDGKFVESKSDKWIDIHNPATNEVIGRVPQATRAEMDAAVASCKRAFPTWADTSVLSRQQLLLRYQQ
          KLFI.GKFVESKSDKWI..HNPATNEVIG.VPQATRAEMDAAVA.CK.AFPT.ADTSVLS.Q.LLL.YQQ
Retrocopy KLFINGKFVESKSDKWIESHNPATNEVIGWVPQATRAEMDAAVAFCKCAFPTRADTSVLSLQHLLLHYQQ

Parental  LIKENLKEIARLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMMGETMPSITKDMDLYSYRLPLGVCA
          LIKENLKEIARLITLEQGKTLADAEGDVFRGLQVVEHACSVT.LMMGETMPSITKDMDLYSYRLPLGVCA
Retrocopy LIKENLKEIARLITLEQGKTLADAEGDVFRGLQVVEHACSVTALMMGETMPSITKDMDLYSYRLPLGVCA

Parental  GIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICD
          GIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSE.VPGATML.AKLLQDSGAPDGTLNIIH.QHEAVNFICD
Retrocopy GIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSE*VPGATMLPAKLLQDSGAPDGTLNIIHRQHEAVNFICD

Parental  HPAIKAISFVGSNQAGEYIFERGSRHGKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMAL
          HPAIKAISFVGSN..GEYIFE.GSRHGKRVQANMGAKNHGVVMPDANKEN.LNQLVGAAFGAAGQRCMAL
Retrocopy HPAIKAISFVGSN*TGEYIFEKGSRHGKRVQANMGAKNHGVVMPDANKENILNQLVGAAFGAAGQRCMAL

Parental  STAILVGDAKKWLPELVERAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDG-RKIN
          STAILVGDAKKWLPELVER.KNLRVNAGDQPGA..GPLITPQAKE.VCNL.DSGTKEGASIL.DG..KIN
Retrocopy STAILVGDAKKWLPELVERTKNLRVNAGDQPGANFGPLITPQAKE*VCNLTDSGTKEGASILFDG>KKIN

Parental  VKGYENGNFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAIFTTNGATARK
          VKGYENGNFVGPTIIS.VKPNMTCYKEEIFGPVLVVLETETLD.AIKIVNDNPYGNGTAIFTTNG.TARK
Retrocopy VKGYENGNFVGPTIISDVKPNMTCYKEEIFGPVLVVLETETLDAAIKIVNDNPYGNGTAIFTTNGPTARK

Parental  YSHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQF-THLKIITSWEVEDATLFPP-AVS
          YSHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQG.QF.T.LK.ITS...EDATL..P..V.
Retrocopy YSHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGFQFYTQLKTITSQWKEDATLSSPVVVM

Parental  RAMGH
          ..MGH
Retrocopy PTMGH

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_2670 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002143	1 retrocopy	retro_chof_869,
Choloepus hoffmanni	ENSCHOG00000002670	1 retrocopy	retro_chof_2670 ,
Choloepus hoffmanni	ENSCHOG00000006418	1 retrocopy	retro_chof_1106,
Xenopus tropicalis	ENSXETG00000013304	1 retrocopy	retro_xtro_56,