RetrogeneDB ID: retro_chof_2592

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_88858:2531..3112(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERTAD4
• Ensembl ID: ENSCHOG00000001750
• Aliases: None
• Description: SERTA domain containing 4 [Source:HGNC Symbol;Acc:25236]

Sequence

>retro_chof_2592
ATGACTGTGGTTCTGTCCATGAACAGAGTCTGCGAGCCCATTGTCTCAGAAGGAGCTGCTGAGATTGCCAGTACCAGACA
CTATGGAGCACGGCTGAGAGCTACGGAGGCCTGGGCCCCACAGGGCCACCCAGGCCCCTCTGCAGAGAGACCCCAGAGCC
TGCCCCCCACTGGCCAGATCACATTACAGGGGAATCTCAAACCCTATAACATCCAAGATCACATACTTCAAGAGGAAGAA
TGTGGAAGAAGAGAATTTTACCCACCTCTCAGATGGTAACCATAAAACCATCTCAGTTTTGAGGAATTAGCTCACATCCT
TCATTATGTCCTTAGAAAAACTAAAGTTTATCGATGATCCTGAAATGTACCTCCAAAGATCTGTCCTTGTAAACAATTTG
ATGAAAAAGATCCATGGAGTAATTATCATGCAGAGTAATTGGTAATTTCCTGCCTGCTCTTTCAATGGTACCTCTGCCTG
AGAATGGCTTATGGCTGAAAACTGTCCACACGGAAAATGACCAAAGGTGGCCAAAGAGGAGTGTGAAGTTTCATGCCTGC
TGCTTTTACCAAGAATGTGGC

Alignment

ORF - retro_chof_2592 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.1 %
• Parental protein coverage: 79.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MTLVLSMNRFCEPIVSEGAAEIAG-YQTLWE-ADSYGGPSPAGP-AQAPLQGDRGARPPLAGSHYRGISN
          MT.VLSMNR.CEPIVSEGAAEIA..YQTLW..A.SYGG..P.GP..QAPLQ.D..A.PPLA.SHYRGISN
Retrocopy MTVVLSMNRVCEPIVSEGAAEIAS<YQTLWSTAESYGGLGPTGP<TQAPLQRDPRACPPLARSHYRGISN

Parental  PITTSKITYFKRKYVEEEDFHPPLSSCSHKTISV-FEERAHILY-MSLEKLKFIDDPEVYLRRSVLINNL
          PIT.SKITYFKRK.VEEE.F...LS...HKTISV.FEE.AHIL..MSLEKLKFIDDPE.YL.RSVL.NNL
Retrocopy PIT-SKITYFKRKNVEEENF-THLSDGNHKTISV<FEELAHILH>MSLEKLKFIDDPEMYLQRSVLVNNL

Parental  MKRIHGAIIMQSNW-FPACSFNGASA-EWLMAENCPHGK-PKVAKEEC-KFHACCFYQECG
          MK.IHG.IIMQSNW.FPACSFNG.SA.EWLMAENCPHGK.PKVAKEEC.KFHACCFYQECG
Retrocopy MKKIHGVIIMQSNW*FPACSFNGTSA*EWLMAENCPHGK*PKVAKEEC>KFHACCFYQECG

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_2592 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001750	2 retrocopies	retro_chof_1540, retro_chof_2592 ,