RetrogeneDB ID: retro_chof_1943

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_428735:302..946(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELAVL4
• Ensembl ID: ENSCHOG00000002464
• Aliases: None
• Description: ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 [Source:HGNC Symbol;Acc:3315]

Sequence

>retro_chof_1943
ACATCCAATACAAGCAGTGGACCCTCCAGCAACAGTAGAAACTGTCCTTCTCCCATGCAGACAGGGGTGGCCACAGATGA
CAGCAAAACCAACCTCATAGTCAATCATTTACCCCAGAATATGACTCAAGAAGAATTTAGGAGTCTCTTTGGTGAAATAG
AATCCTGTGAACTCATGAGAGACAAAATTACAGGACAGAGTTTAGGGTATGGATTTGTTAACTATATTGATGCAAAGGAT
GCAGAAAAAGCCGTCAACAATTTAAATGGACTCCGACTTCAGACCAAAACCATAAAGGTCTCATATGCCTGTCCAAGCTC
TGCCTCAATCAGGGATGCTAACCTCTATGTTAGTGGCCTTCCCAAAACCACAAACCAGAAGGAACTGGAGCAGCTTTTCT
CACAATATGGCTGTATCATCACCTCATGAATCCTGGTTGATCAAGTCACAGGGGTGTCCAGAGGGGTGGGATTCATCCGC
TTTGATAAGAGGATTGAGGCAGAGGAAGCTATCAAGTGTTGAATGGCCAGAAGCCCAGTGGTGCTACAGAACCGATTACT
GTGAAGTTTACCAATAACCCCAGCCAGAAGTCCAGCCAGGCTCTGCTCTCCCAGCTCTACCAGTCCCCTAACTGGTGCTA
TCCT

Alignment

ORF - retro_chof_1943 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.04 %
• Parental protein coverage: 56.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSNTSNGPSSNSRNCPSPMQTGAATDDSKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQS
          TSNTS.GPSSNSRNCPSPMQTG.ATDDSKTNLIVN.LPQNMTQEEFRSLF...GEIESC.L.RDKITGQS
Retrocopy TSNTSSGPSSNSRNCPSPMQTGVATDDSKTNLIVNHLPQNMTQEEFRSLF---GEIESCELMRDKITGQS

Parental  LGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYG
          LGYGFVNYID.KDAEKA.N.LNGLRLQTKTIKVSYA.PSSASIRDANLYVSGLPKT..QKELEQLFSQYG
Retrocopy LGYGFVNYIDAKDAEKAVNNLNGLRLQTKTIKVSYACPSSASIRDANLYVSGLPKTTNQKELEQLFSQYG

Parental  RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK-GLNGQKPSGATEPFTVKFANNPSQK-SQALLSQL
          .IITS.ILVDQVTGVSRGVGFIRFDKRIEAEEAIK..LNGQKPSGATEP.TVKF.NNPSQK.SQALLSQL
Retrocopy CIITS*ILVDQVTGVSRGVGFIRFDKRIEAEEAIK<VLNGQKPSGATEPITVKFTNNPSQKSSQALLSQL

Parental  YQ-PNRRYP
          YQ.PN..YP
Retrocopy YQSPNWCYP

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_1943 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002464	1 retrocopy	retro_chof_1943 ,
Choloepus hoffmanni	ENSCHOG00000005327	3 retrocopies	retro_chof_1150, retro_chof_1182, retro_chof_1274,
Choloepus hoffmanni	ENSCHOG00000006810	2 retrocopies	retro_chof_2564, retro_chof_44,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Cavia porcellus	ENSCPOG00000002044	1 retrocopy	retro_cpor_1379,
Macropus eugenii	ENSMEUG00000007145	1 retrocopy	retro_meug_426,
Sarcophilus harrisii	ENSSHAG00000013832	1 retrocopy	retro_shar_78,