RetrogeneDB ID: retro_tsyr_88

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_2472:240871..241440(-)
• Located in intron of: ENSTSYG00000002409

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD1
• Ensembl ID: ENSTSYG00000000812
• Aliases: None
• Description: copper metabolism (Murr1) domain containing 1 [Source:HGNC Symbol;Acc:23024]

Sequence

>retro_tsyr_88
ATGGCGGGTGAGCTTGAGGGCTGCAAGCCCCTGAGCAGGCTGCTGAGCGGTCTGGCCCAGGACAATTTCTTCCGGCACCC
GGGCATCACAGAGGAGCTGCTGCGGAGCCAACTCTATCCGGAGGTGCCACCCGAGGAGTTCCGTCCCTTTCTGGCGAAGA
TGAGGGGGGATTCTGAAGTCTATTGCATCAGGAGACATGGATTTCAATCAGCTGGAGGCATTCTTGACTGCCCAAACCAA
AAAGCAAGGTGGAATCACATCTGACCAAGCTGCTGTCATTTCCAAATTCTGGAAGAGCCACAAGACCAAAATCCAAGAGA
GCCTCATGAACCAGAGCCGCTGGGATAATGGGCTTCACGGTCTGAACTGGAGAGTTGATGGCAAGTCTCAGTCAAGGCAT
TCATCTCAAATACATACCCCTGTTGCCATTATAGAGCTGGAATTAGGGAAAAGTGGACAGGAATCTGAATATCTGTGTTT
GGAATTTGATGAGGTCAAGGTCAACCAAGTTCTGAAGAAGCTCTCAGTGGTAGAAGAAAGTATCAGCACACTGATGCAGC
CAGCCTAAC

Alignment

ORF - retro_tsyr_88 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGELEGCKPLSGLLSGLAQDNFFRHPGITEELLRSQLYPEVPPEEFRPFLAKMRG-ILKSIASGDMDFN
          MAGELEGCKPLS.LLSGLAQDNFFRHPGITEELLRSQLYPEVPPEEFRPFLAKMRG.ILKSIASGDMDFN
Retrocopy MAGELEGCKPLSRLLSGLAQDNFFRHPGITEELLRSQLYPEVPPEEFRPFLAKMRG>ILKSIASGDMDFN

Parental  QLEAFLTAQTKKQGGITSDQAAVISKFWKSHKTKIRESLMNQSRWDNGLRGLNWRVDGKSQSRHSSQIHT
          QLEAFLTAQTKKQGGITSDQAAVISKFWKSHKTKI.ESLMNQSRWDNGL.GLNWRVDGKSQSRHSSQIHT
Retrocopy QLEAFLTAQTKKQGGITSDQAAVISKFWKSHKTKIQESLMNQSRWDNGLHGLNWRVDGKSQSRHSSQIHT

Parental  PVAIIELELGKSGQESEYLCLEFDEVKVNQVLKKLSEVEESISTLI-SQPN
          PVAIIELELGKSGQESEYLCLEFDEVKVNQVLKKLS.VEESISTL..SQPN
Retrocopy PVAIIELELGKSGQESEYLCLEFDEVKVNQVLKKLSVVEESISTLM>SQPN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_88 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003090	1 retrocopy	retro_cfam_343,
Cavia porcellus	ENSCPOG00000002088	1 retrocopy	retro_cpor_482,
Mustela putorius furo	ENSMPUG00000005842	1 retrocopy	retro_mputfur_1120,
Ictidomys tridecemlineatus	ENSSTOG00000015062	1 retrocopy	retro_itri_562,
Tarsius syrichta	ENSTSYG00000000812	1 retrocopy	retro_tsyr_88 ,