RetrogeneDB ID: retro_tbel_167

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1363:946158..947468(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP5M1
• Ensembl ID: ENSTBEG00000010976
• Aliases: None
• Description: adaptor-related protein complex 5, mu 1 subunit [Source:HGNC Symbol;Acc:20192]

Sequence

>retro_tbel_167
CCCTTTCTTAGAGCAGTACTCTTCAAACTTAGATTATTGGATGATGATGAAGACTTCATGGAGAGCCGTGAGAGTTGTTC
ACACATCAATAAAATGTCCATCTATGTCATTGTAGGAGGTGAAGAGCTCTGGTCGGTTGTTGCTTTTCTAGAGAATAGCA
TGATAGATGCTTGTATTCCACTAGTTGAGCAAACTCTCTCCCCTCATCCACTGTTAACTAACTTTAGTGGAATTTCACAA
GGCTTTGAACTGCTTTTTGGGATACAAGATTTTCTTTACTCAGGTCAAAAAAGTGACAGTGAGTTAAATGCAAAATTGAA
CCAGTTACCTGACCTGCTTCTGTAGACGTGTGCATTTGGCACTTTATTAGATGCCGACTCGCAGAATTCACTGGCTAATA
TTAACTTTGCTTCTGTGACCCACCCACACAGACAGCCAGCCTGGAGAGCTGGGACATACAAAGGACAACCACAGGTTTCT
ATTTCCATCACACAAAAGGTAAAATCCACACAATATGATGAACAGGATGTAGTGGATACCTGGCAAGTTGTTGGAACCGG
TGCTTGCAAGTGTGATTTGGAAGGAGTCATGTCAAATGTTACCATCAGCTTGAGTCTCCCCACCAATGGATTGCCACTTC
AAGATGTTCCAGTTCATCCTTCTCTTGACTCTGCCATTCTTACTTCTAGTAGCATTGATGCAATGGATGATTCTGCATTT
AGTGGGCCTTATAAACTTCCATTCACTCCACCTTCAGAATCATTCCACTTGTGTCACTATTCTTCCCAGGTCCCTATCCC
ACCAATTTTGGGTTTTTATCAAGTGAAAGAGGAAAAGTACAACTAAAAATAGCAATTAATTTAAAACTTCATGAAAGTGT
GAAAAATAATTTTGAATTTTGTGAAGCTCATATACCCTTTTACAATAGAGGTCCAATTACACATTTGGGATACAAAGTTA
GTTTTGGCCAGCTTGAAGTATTTCGAAAGAAAAACTTATTAATCTGGGTTATTGGCCGGAAGTTTCCAAAATCAATGGGA
ATTAATCTTTCTGGAACTATAACTTTTGGAACCAAGAATCAAGAGAAGCAGCCATTTGACCAGATTTGTATTGGAGGTAC
AGCATATTTAAAGCTTCATTTTAAGAACTTAGATTGCACACTCACTGGGTGTTATGCGGATCAGCATTCAGTTCAAGTTT
TTGCATCAGGAAAACCAAAAATAAGTACACACCGGAAACTAATTTCTTCTGATTATTACATCTGGAATTCTAAAGCACCT
GCTCCAGTAACATATGGATCATTATTACTA

Alignment

ORF - retro_tbel_167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.56 %
• Parental protein coverage: 90. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PFLKAVLFELRLLDDDKDFMESRDSCSHINKTSIYGLTVGSEELWPVVAFLKNSMIYACVPLVEQTLSPH
          PFL.AVLF.LRLLDDD.DFMESR.SCSHINK.SIY...VG.EELW.VVAFL.NSMI.AC.PLVEQTLSPH
Retrocopy PFLRAVLFKLRLLDDDEDFMESRESCSHINKMSIY-VIVGGEELWSVVAFLENSMIDACIPLVEQTLSPH

Parental  PPLINISGISQGFELLFGIQDFLYSGQKSDSELNAKLNQLPDLLLQACPFGTMLDANFQNSLDNINFASV
          P.L.N.SGISQGFELLFGIQDFLYSGQKSDSELNAKLNQLPDLLL..C.FGT.LDA..QNSL.NINFASV
Retrocopy PLLTNFSGISQGFELLFGIQDFLYSGQKSDSELNAKLNQLPDLLL*TCAFGTLLDADSQNSLANINFASV

Parental  THPQKQPAWRAGTYKGKPQVSISITEKVKSMQYDKQDIADTWQVVGTVTCKCDLEGVMPNVTISLSLPTN
          THP..QPAWRAGTYKG.PQVSISIT.KVKS.QYD.QD..DTWQVVGT..CKCDLEGVM.NVTISLSLPTN
Retrocopy THPHRQPAWRAGTYKGQPQVSISITQKVKSTQYDEQDVVDTWQVVGTGACKCDLEGVMSNVTISLSLPTN

Parental  GSPLQDILVHPCVTSLDSAILTSSSIDAMDDSAFSGPYKFPFTPPLESFNLCHYTSQVPVPPILGFYQVK
          G.PLQD..VHP...SLDSAILTSSSIDAMDDSAFSGPYK.PFTPP.ESF.LCHY.SQVP.PPILGFYQVK
Retrocopy GLPLQDVPVHP---SLDSAILTSSSIDAMDDSAFSGPYKLPFTPPSESFHLCHYSSQVPIPPILGFYQVK

Parental  EEE-VQLKIAINLKLHESVKNNFEFCEAHIPFYNRGPITHLEYKISFGQLEVFREKSLLIWVIGQKFPKS
          EE..VQLKIAINLKLHESVKNNFEFCEAHIPFYNRGPITHL.YK.SFGQLEVFR.K.LLIWVIG.KFPKS
Retrocopy EEK<VQLKIAINLKLHESVKNNFEFCEAHIPFYNRGPITHLGYKVSFGQLEVFRKKNLLIWVIGRKFPKS

Parental  MEINLSGTITFGTKNQEKQPFDQICIGGTAYLKLHFKILDYTLTGCYADQHSVQVFASGKPKISTHRKLI
          M.INLSGTITFGTKNQEKQPFDQICIGGTAYLKLHFK.LD.TLTGCYADQHSVQVFASGKPKISTHRKLI
Retrocopy MGINLSGTITFGTKNQEKQPFDQICIGGTAYLKLHFKNLDCTLTGCYADQHSVQVFASGKPKISTHRKLI

Parental  SSDYYIWNSKAPAPVTYGSLLL
          SSDYYIWNSKAPAPVTYGSLLL
Retrocopy SSDYYIWNSKAPAPVTYGSLLL

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_167 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_167 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 ,