RetrogeneDB ID: retro_itri_993

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393357.1:1347733..1348657(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP5M1
• Ensembl ID: ENSSTOG00000011073
• Aliases: None
• Description: adaptor-related protein complex 5, mu 1 subunit [Source:HGNC Symbol;Acc:20192]

Sequence

>retro_itri_993
CGTTATCCAACCGTTGAAAAGAGAGCCAAAGTATTCAATGGAGCAAGTTATGTGCCTATTCCTGAAGATGGTCCCTTTCT
TAAAGAACTTAGATTATTAGATGACGATAAGGACTTCGTAGAGCGTCATGATTGTTGTACCCACATCAATAAAACAACCA
TCTATAGACTTTCAGTAGGAGGTGAAGAACTCTGGCCAGTGGTTGCTTTTCTGAAGAATGGCATGATATATGCTAGTGTT
CCACTTGTTGAACAAACTCTTTCCCCTCATCCACCATTAATTAGCATCAGTGGAATTTCACAAGGCTTGGAACTTCTTTT
TGATATACAGGGTTTTCTTTATTCTAGTCAAAAAAATGATACTGGGCTAAACACAAAATTGAGCCAGTTGCCTAATTTGC
TTCTTCAGGCTTCTCCATTTGGTACTTTATTAGATGCCAACTTACAGAATTCATTGGATAACATTAATTTTGCTTCTGTG
TCTCAGCCACAGAAACAGCCAGCTTGGAAAGTTGGAACATACAAAGGAAAACCACAGGTTTCTATTTCTATCACTGAAAA
GGTAAAATCCATGCAATATGATAAACGGGATATAGAAGATACATGGCAAGTTGTTGGAGCAGTCATTTTCAAGTGTGATT
TAGAAGGAATCATGCCAAATGTCACCATCAGCTTGAACCTCCCCACCAATGGATTTCCACTTCAAGATATTCTAGTTCAT
CCTTGTGTGACTTCTCTTGATTCTGCCATTCTGACCTCTAGCAACATTGATGCAGTGGATGATTCTGCCTTTAGTGGGCC
TTATAAATTTCCATTCACTCCACCATTAGAGTCATTCAATTTATGCTACTATACTTCCCAGGTCCCCGTACCACCAATTT
TGGGTTTCTATCAATTGAAAGAATAAGAAATACAACTAAAAATA

Alignment

ORF - retro_itri_993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.59 %
• Parental protein coverage: 63.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYPTVEKRAKVFNGASYVPIPEDGPFLKALLFELRLLDDDKDFVERRDSCTHINKTTIYRLSVGGEELWP
          RYPTVEKRAKVFNGASYVPIPEDGPFLK....ELRLLDDDKDFVER.D.CTHINKTTIYRLSVGGEELWP
Retrocopy RYPTVEKRAKVFNGASYVPIPEDGPFLK----ELRLLDDDKDFVERHDCCTHINKTTIYRLSVGGEELWP

Parental  VVAFLKNGMIYASVPLVEQTLSPRPPLISISGISQGLELLFGIQDFLYSSQKNDTELNTKLSQLPNLLLQ
          VVAFLKNGMIYASVPLVEQTLSP.PPLISISGISQGLELLF.IQ.FLYSSQKNDT.LNTKLSQLPNLLLQ
Retrocopy VVAFLKNGMIYASVPLVEQTLSPHPPLISISGISQGLELLFDIQGFLYSSQKNDTGLNTKLSQLPNLLLQ

Parental  ACPFGTLLDANLQNSLDNINFASVSQPQKQPAWKAGTYKGKPQVSVSITEKVKSMQYDKQDIADTWQVVG
          A.PFGTLLDANLQNSLDNINFASVSQPQKQPAWK.GTYKGKPQVS.SITEKVKSMQYDK.DI.DTWQVVG
Retrocopy ASPFGTLLDANLQNSLDNINFASVSQPQKQPAWKVGTYKGKPQVSISITEKVKSMQYDKRDIEDTWQVVG

Parental  AVICKCDLEGIMPNVTISLNLPTNGSPLQDILVHPCVTSLDSAILTSSSIDAVDDSAFSGPYKFPFTPPL
          AVI.KCDLEGIMPNVTISLNLPTNG.PLQDILVHPCVTSLDSAILTSS.IDAVDDSAFSGPYKFPFTPPL
Retrocopy AVIFKCDLEGIMPNVTISLNLPTNGFPLQDILVHPCVTSLDSAILTSSNIDAVDDSAFSGPYKFPFTPPL

Parental  ESFNLCYYTSQVPVPPILGFYQMKEEEIQLKI
          ESFNLCYYTSQVPVPPILGFYQ.KE.EIQLKI
Retrocopy ESFNLCYYTSQVPVPPILGFYQLKE*EIQLKI

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_993 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_993 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002388	1 retrocopy	retro_amel_1700,
Canis familiaris	ENSCAFG00000015249	1 retrocopy	retro_cfam_1676,
Mustela putorius furo	ENSMPUG00000005943	1 retrocopy	retro_mputfur_210,
Nomascus leucogenys	ENSNLEG00000013007	1 retrocopy	retro_nleu_590,
Ictidomys tridecemlineatus	ENSSTOG00000011073	1 retrocopy	retro_itri_993 ,
Tupaia belangeri	ENSTBEG00000010976	1 retrocopy	retro_tbel_167,