RetrogeneDB ID: retro_chof_2604

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_89760:5552..6001(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GATAD1
• Ensembl ID: ENSCHOG00000000193
• Aliases: None
• Description: GATA zinc finger domain containing 1 [Source:HGNC Symbol;Acc:29941]

Sequence

>retro_chof_2604
AAAAGACAAATTTTTAAGTTAAAAAATTCTGTCAAAGCTCCTGAGTCAGTTTCTACCATCATTACTACAGAATCAATCTC
TACAAGGGAGTGTATTGCCAAATTGGAGATGTTTCTGTGATTGATTAACAGGATGGAAAACTCTTTTATGTTCAGATCAG
AGATTTCACCCAGGATCAGCATTGTGAGGAGAGTGCAGCCCTGACATGGCTCATTCTCATCCTCTCTAGCCCCAGAGACC
AATTTGATCCCATATTGTATATCCTAGGACCAGAGGACTATTATGCAAGGAAAATGGAATACTTGGAATTTGTTTATCAT
GCACCTTCTGAATATTTCAAGTAATGATCATCACCAATTCCATTTCCTACCAGACCACAGAAAGGCTATATATGGACTCA
CATTGGACCTAGTGCTAATGAACTATTAAGGACACTTGCCAACCCTTTG

Alignment

ORF - retro_chof_2604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.08 %
• Parental protein coverage: 82.26 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRHIFKLKNPIKAPESVSTIITAESI-FYKGVYYQIGDVVSVIDEQDGKPYYAQIRGFIQDQYCEKSAAL
          .R.IFKLKN..KAPESVSTIIT.ESI..YKGVY.QIGDV.SVID.QDGK..Y.QIR.F.QDQ.CE.SAAL
Retrocopy KRQIFKLKNSVKAPESVSTIITTESI<LYKGVYCQIGDV-SVID*QDGKLFYVQIRDFTQDQHCEESAAL

Parental  TWLIPTLSSPRDQFDPASYIIGPEEDLPRKMEYLEFVCHAPSEYFKSRSSPFPTVPTRPEKGYIWTHVGP
          TWLI..LSSPRDQFDP..YI.GPE....RKMEYLEFV.HAPSEYFK..SSP.P..PTRP.KGYIWTH.GP
Retrocopy TWLILILSSPRDQFDPILYILGPEDYYARKMEYLEFVYHAPSEYFK**SSPIP-FPTRPQKGYIWTHIGP

Parental  TPAITIKETVANHL
          ..A.....T.AN.L
Retrocopy S-ANELLRTLANPL

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_2604 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 4 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000193	2 retrocopies	retro_chof_2074, retro_chof_2604 ,
Dipodomys ordii	ENSDORG00000005895	10 retrocopies	retro_dord_267, retro_dord_270, retro_dord_300, retro_dord_318, retro_dord_363, retro_dord_459, retro_dord_463, retro_dord_504, retro_dord_551, retro_dord_566,
Monodelphis domestica	ENSMODG00000010701	1 retrocopy	retro_mdom_877,
Oryctolagus cuniculus	ENSOCUG00000014806	1 retrocopy	retro_ocun_1772,