RetrogeneDB ID: retro_tbel_3

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5827:524021..525536(+)
• Located in intron of: ENSTBEG00000012379

Retrocopy information

• Ensembl ID: ENSTBEG00000012453
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000013569
• Aliases: None
• Description: None

Sequence

>retro_tbel_3
AATGGCCAAAGTTTTCTGGTCTTGGATGAACAAATGTTTGCAAAAGAAATTCTTCCCAAGTACCTCAAGCACAATAACAT
GGCGAGCTTTGTGAGGCAGCTGAATATGCATGGTTTCCGTAAAGTAGTACACACTGACTCTGGAATTATAAAGCAGAAAA
GAGATGGTCCTGTTGAATTTCAGCATCCTTACTTCAAGCAAGGCCAGGATGACTTGTTAGAGAACATTAAAAGGAAGGTT
TCATCTTCAAATCCAGAAGAAAATAAAATTCGTCAGGAAGATTTAACAAAAATTATAAATAGTGCTCAGAAGGTTCAAAT
AAAACGAGAAACTATTGAATCCAGGCTTTCTGAATTAAAAAGTGAGAATGAATCCCTTTGGAAAGAAGTGTCAGAGTTAC
GGGCAACACATGCACAACAACAAGTTATTCGAAAGATTGTCCAGTTTATTGTTACATTGGTTCAGAATAATCGGCTTGTG
AATTTAAAACGTAAAAGGCCTCTACTTCTGAATACTAATGGAGCCCAAAAGAAGAATCTGTTTCTACACATAATCAAAGA
ACCAACTGATAATCACCATCATAAAGTTCCACACAGTAGGACTGAAGGTTTAAAGCTAAGAGAACGGATTTCAGGTGACA
TCATTATTTATGATGTTACTGACGATAATGCGGATGAAGAAAATATCTCAGTTATTCCAGAAACTAATGAGGATGTTATA
TCTGATCCTTCCAGTTGTAGCCAGTACCCTGATGTTGTCATTGCTGAAGATGACAATGAAGATGAATATGCACCTGTTAT
TCAGAGTGGAGATCAGAGTGGACCAGCCAGAGCATCCTTAAGTTCAGGCAGTGATGGCACCAGCCCACTCATGTCTAGTG
CTGTCCAACTAAATGGCTCAGCCAGCTTGACCACAGAAGATCCTGTGTCCATGATGGATTCTATGTTGAATGATAACATT
AATCTCTTGGGAAAGCTTGAGCTGTTGGATTATCTTGACAGTATTGATTACAGTTTGGAGGACTTCCAAGCCATGCTGTC
AGGAAAACAGTTTAGCACAGACCCAGATCTCCTGGTTGATCTTTTCACTAGTTCTCTGCAGATGAATCCCACAGATTACA
TCAATAATACAAAATCTGGGAATAAAGGATTAGAAACCTCCAAGAACAATGTAGTTCAGCCAGCTTCAGAAGAGGGAAGA
AAATCTAAATCCAAACCAGATAAGCAGCTTATCCAGTACACTGCTTTTCCACTTCTTGCATTCCTCGATGGGAACCCTGC
TTCCACTGTTGAACAGGGGGGTACACCAGCATCATCAGAAGCCATGACCTCTGTAGATAAACCCATAGAAGTTGATGAGC
TTCTGGATAGCAGCCTGGACCCAGAACCAACCCAGAATAAGCTCGTTCACCTGGAGCCATTGACTGAAGCTGAAGCTAGG
GAAGCTACACTGTTTTATTTATGTGAACTTGCTCCCGCACCTCTGGATAGTGATATGCCACTTTTAGATAGCTAA

Alignment

ORF - retro_tbel_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.48 %
• Parental protein coverage: 94.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGQSFLVLDEQRFAKEILPKYFKHNNMASFVRQLNMYGFRKVVHIDSGIVKQERDGPVEFQHPYFKQGQD
          NGQSFLVLDEQ.FAKEILPKY.KHNNMASFVRQLNM.GFRKVVH.DSGI.KQ.RDGPVEFQHPYFKQGQD
Retrocopy NGQSFLVLDEQMFAKEILPKYLKHNNMASFVRQLNMHGFRKVVHTDSGIIKQKRDGPVEFQHPYFKQGQD

Parental  DLLENIKRKVSSSKPEENKIRQEDLTKIISSAQKVQIKQETIESRLSELKSENESLWKEVSELRAKHAQQ
          DLLENIKRKVSSS.PEENKIRQEDLTKII.SAQKVQIK.ETIESRLSELKSENESLWKEVSELRA.HAQQ
Retrocopy DLLENIKRKVSSSNPEENKIRQEDLTKIINSAQKVQIKRETIESRLSELKSENESLWKEVSELRATHAQQ

Parental  QQVIRKIVQFIVTLVQNNQLVSLKRKRPLLLNTNGAQKKNLFQHIVKEPTDNHHHKVPHSRTEGLKPRER
          Q.VIRKIVQFIVTLVQNN.LV.LKRKRPLLLNTNGAQKKNLF.HI.KEPTDNHHHKVPHSRTEGLK.RER
Retrocopy Q-VIRKIVQFIVTLVQNNRLVNLKRKRPLLLNTNGAQKKNLFLHIIKEPTDNHHHKVPHSRTEGLKLRER

Parental  ISDDIIIYDVTDDNADEENIPVIPETNEDVISDPSGCSQYPDIVIVEDDNEDEYAPVIQSGDQSEPARES
          IS.DIIIYDVTDDNADEENI.VIPETNEDVISDPS.CSQYPD.VI.EDDNEDEYAPVIQSGDQS.PAR.S
Retrocopy ISGDIIIYDVTDDNADEENISVIPETNEDVISDPSSCSQYPDVVIAEDDNEDEYAPVIQSGDQSGPARAS

Parental  LSSGSDCTSPLMSSAVQLNGSSSLTTEDPVTMMDSILNDNINLLGKVELLDYLDSIDCSLEDFQAMLSGR
          LSSGSD.TSPLMSSAVQLNGS.SLTTEDPV.MMDS.LNDNINLLGK.ELLDYLDSID.SLEDFQAMLSG.
Retrocopy LSSGSDGTSPLMSSAVQLNGSASLTTEDPVSMMDSMLNDNINLLGKLELLDYLDSIDYSLEDFQAMLSGK

Parental  QFSIDPDLLVDLFTSSVQMNPTDYINNTKSENKGLETSKNNVVQPASEEGRKSKSKPDKQLIQYTAFPLL
          QFS.DPDLLVDLFTSS.QMNPTDYINNTKS.NKGLETSKNNVVQPASEEGRKSKSKPDKQLIQYTAFPLL
Retrocopy QFSTDPDLLVDLFTSSLQMNPTDYINNTKSGNKGLETSKNNVVQPASEEGRKSKSKPDKQLIQYTAFPLL

Parental  AFLDGNPASTVEQGGTPASSEAMSSVDNPIEVDELLDSSLDPEPTQSKLVRLEPLTEAEASEATLFYLCE
          AFLDGNPASTVEQGGTPASSEAM.SVD.PIEVDELLDSSLDPEPTQ.KLV.LEPLTEAEA.EATLFYLCE
Retrocopy AFLDGNPASTVEQGGTPASSEAMTSVDKPIEVDELLDSSLDPEPTQNKLVHLEPLTEAEAREATLFYLCE

Parental  LAPAPLDSDMPLLDS
          LAPAPLDSDMPLLDS
Retrocopy LAPAPLDSDMPLLDS

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_3 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010951	1 retrocopy	retro_chof_621,
Cavia porcellus	ENSCPOG00000007509	1 retrocopy	retro_cpor_1341,
Macaca mulatta	ENSMMUG00000007910	1 retrocopy	retro_mmul_867,
Tupaia belangeri	ENSTBEG00000013569	3 retrocopies	retro_tbel_1029, retro_tbel_19, retro_tbel_3 ,