RetrogeneDB ID: retro_tbel_2282

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_108489:81776..83323(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAPD5
• Ensembl ID: ENSTBEG00000012515
• Aliases: None
• Description: PAP associated domain containing 5 [Source:HGNC Symbol;Acc:30758]

Sequence

>retro_tbel_2282
AGCGGAACGACGTGGAAGCGGAGGAACTGCACCCAGGGAGTCGTGGGTCTTCATGAAGAAATCGGTGATTTTTATGAACA
CATGTCTCCAAGACCTGAGGAGGAGAAGATGCGGATGGAGGCGGTGACAGGATTGAGAGCGTGACCAAGGAGCTCTGGCC
CTGTGCTGATGTCCAGATATTTGGAAGTTTTAAAACTGACCTATATTGACCTACTAGTGGCATCGATCGTGTGGTGTTTG
GAAAGTGGGAGAATCTACCCCTCTGGACCCTGGAAGAAGCTCTTCGGAAACATAAAGTTGCAGATGAAGAATTCAGTGAA
AGTTCTAGACAAGGCAACTGTACTTATTATCAAATTAATAGATTCTTTTACTGAAGTGAAAGTTGATATCCGCTTTAATG
TACAGAATGGCGTGAGAGCAGCTGACCTCATCAAAGATTTTACCAAGAACTATCCTGTATTGCCATATTTGGTTTTAGTA
TTGAAACGATTCTTATTACAGAGGGACCTTAATGAAGTATTTACAGGTGGAATTGGTTCTTATAGTCTCTTTTTAACGGC
TGTCCGCTTCCTTCAGTTACATCCCAGGGAAGATGCTTGCATCCCCAACACAAACTCTGGTGTTCTCTTACTACAATTTT
TTGAATTGTATGGACGACACTTCAATTATTTAAAGACTGGCATCCAGATAAAGGATGGTGGTTCACTTGTGGCCAAAGAT
GAAGAACAAAAAAATATGCTAGATGGCTACAGGCCATCGATGCTTTATATGGAAGATCCTTTACAACCAGGGAATGATGC
TGGAAGGAGTTCATACGGGGCCATGCAAGCGAAACGGGCCTTCGATTACGCCTCCGTTGTTCTGAGCCATGCCGTATTGC
CAATAGCAAAGTACTACCCCAACAACGAAACAGAGAGCATATTAGGTAGAATAATTAGAGTAACGGATGAAGTCGCCACG
TACAGAGATTGGATATCAAAGCAGTGGGGCTTGCAGAATAGGCCTGAGCCTTCATGCAACAGAAATGGTGTTACCTTGAT
AGTAGATACTCAGCAGTTAGATAAATGTAATAATAACCTCTCTGAAGAAAATGAAGCCCTTGGAAAATGCAGAAGTAAAA
CTTCGGAATCTCTTAGTGAACCCTCTTCAAACTCTTCATCAGGTCCAGTGTCGTCCTCTTCTGCCATGCAGTCCAGCTCT
AGTGATGTAGATTCCGACGTGACACCATGCAAAACTCCGAAACAGCTGCTCTGCTGGCCGTCTGCTGGGAACTGAGTAGG
ATCTCAAGACGTGTCCTTGGAGTCCTCTCTGGCAGTTGGGAAAATGCAGAGCACCCAAACCACTAACACGTCCAACAGTA
CCAACAAACCCCAGCATGGATCAGCAAGGCTCTTTCGTTCTTCCAGCAAAGGCTTCCAAGGTACAACTCAAACAAGCCAT
GGTTCCTTGATGACAAACAAACAGCATCAAGGCAAATCCAGTAATCAGTATTACCATGGTAAAAAGAGAAACACCGGAGG
GACGTGCCCCTCTCAGACCTCTGTAGA

Alignment

ORF - retro_tbel_2282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.75 %
• Parental protein coverage: 85.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SGTPWKRRKCNQGVVGLHEEISDFYEYMSPRPEEEKMRMEVV-NRIESVIKELWPSADVQIFGSFKTGLY
          SGT.WKRR.C.QGVVGLHEEI.DFYE.MSPRPEEEKMRME.V..RIESV.KELWP.ADVQIFGSFKT.LY
Retrocopy SGTTWKRRNCTQGVVGLHEEIGDFYEHMSPRPEEEKMRMEAV<DRIESVTKELWPCADVQIFGSFKTDLY

Parental  LPTSDIDLVVFGKWENLPLWTLEEALRKHKVADED-SVKVLDKATVPIIKLTDSFTEVKVDISFNVQNGV
          .PTS.ID.VVFGKWENLPLWTLEEALRKHKVADE..SVKVLDKATV.IIKL.DSFTEVKVDI.FNVQNGV
Retrocopy *PTSGIDRVVFGKWENLPLWTLEEALRKHKVADEE>SVKVLDKATVLIIKLIDSFTEVKVDIRFNVQNGV

Parental  RAADLIKDFTKKYPVLPYLV-VLKQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQLHPREDACIPNTNYGV
          RAADLIKDFTK.YPVLPYLV.VLK.FLLQRDLNEVFTGGIGSYSLFL.AV.FLQLHPREDACIPNTN.GV
Retrocopy RAADLIKDFTKNYPVLPYLVLVLKRFLLQRDLNEVFTGGIGSYSLFLTAVRFLQLHPREDACIPNTNSGV

Parental  LLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPSMLYIEDPLQPGNDVGRSSYGAMQVK
          LL..FFELYGRHFNYLKTGI.IKDGGS.VAKDE.QKNMLDGYRPSMLY.EDPLQPGND.GRSSYGAMQ.K
Retrocopy LLLQFFELYGRHFNYLKTGIQIKDGGSLVAKDEEQKNMLDGYRPSMLYMEDPLQPGNDAGRSSYGAMQAK

Parental  QAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIRVTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIV
          .AFDYA.VVLSHAV.PIAKYYPNNETESILGRIIRVTDEVATYRDWISKQWGLQNRPEPSCN.NGVTLIV
Retrocopy RAFDYASVVLSHAVLPIAKYYPNNETESILGRIIRVTDEVATYRDWISKQWGLQNRPEPSCNRNGVTLIV

Parental  DTQQLDKCNNNLSEENEALGKCRSKTSESLSKHSSNSSSGPVSSSSATQSSSSDVDSDATPCKTPKQLLC
          DTQQLDKCNNNLSEENEALGKCRSKTSESLS..SSNSSSGPVSSSSA.QSSSSDVDSD.TPCKTPKQLLC
Retrocopy DTQQLDKCNNNLSEENEALGKCRSKTSESLSEPSSNSSSGPVSSSSAMQSSSSDVDSDVTPCKTPKQLLC

Parental  RPSAGNRVGSQDVSLESSPAVGKMQSTQTTNTSNSTNKPQHGSARLFRSSSKGFQGTTQTSHGSLMTNKQ
          .PSAGN.VGSQDVSLESS.AVGKMQSTQTTNTSNSTNKPQHGSARLFRSSSKGFQGTTQTSHGSLMTNKQ
Retrocopy WPSAGN*VGSQDVSLESSLAVGKMQSTQTTNTSNSTNKPQHGSARLFRSSSKGFQGTTQTSHGSLMTNKQ

Parental  HQGKSNNQYYHGKKR-KHKRDAPLSDLCR
          HQGKS.NQYYHGKKR.KH.RD.PLSDLCR
Retrocopy HQGKSSNQYYHGKKR<KHRRDVPLSDLCR

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_2282 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2282 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000012515	1 retrocopy	retro_tbel_2282 ,