RetrogeneDB ID: retro_tbel_19

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4523:263447..264905(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000007814
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_tbel_19
AAGTACCTCAAGCACAATAACGTGGTAAGCTTTGTGAGGCAGCTGAATATGCATGGTTTCCGTAAAGTAGTACATACGGA
CTCTGGAATTGTAAAGCAGGAAAGAGATGGTCCTGTTGAATTTCAGCATCCTTACTTCAAACAAGGCCAGGATGAATTGC
TAGAGAACATTAAAAGGAAGGTTTCATCTTCCAAACCAGAAGAAAATAAAATTCGTCAGGAAGATTTAACAAAAATTATA
AGTAGTGCTCAGAAGGTTCAAATAAAACAAGAAACTATTGAATCCAGGCTTTCTGAATTAAAAAGTGAGAATGAGTCCCT
TTGGAAAGAAGTATCAGAGTTACGGGCAAAACATGCACAACGACAAGTTATTCGAAAGATTGTCCAGTTTATTGTTACAT
TGGTTCAGAATAACCAGCTTGTGAGTTTAAAACGTAAAAGGCTTCTACTTCTGAATACTAACAGAGCCCAAAAGAAGAAT
CTGTTTCGACACATAGTCAAAGAACCAACTGATAATCACCATCATAAAGTTCCACACAGTAGGACTGAAGGTTTAGAGCC
AAGAGAATGGATTTCAGATGACATCATTATTTATGATGTTACTGACGATAATGCGGATGAAGAAAATATTCCAGTTATTC
CAGAAACTAATGAGGATGTTATATCTGATCCCTCCAGTTGTAGCCAGTACCCTGATGTTGTCATTGTTGAAGATGACTAT
GAAGATGAATATGCACCTGTTATTCAGAGTGGAGATCAGAGTGAACCAGCCAGAGAATCCCTAAGTTCAGGCAGTGATTG
CACCAGCCCACTCATGTCTAGTGCTATCCAGCTAAATGGCTCATCCAGCTTGACCACTGAAGATCCTGTGACCATGATGG
ATTCTATATTGAATGATAACATTAATCTCTTGGGAAAGGTTGAGCTGTTGGATTATCTTGACAGTATTGATTACAGTTTA
GAGGACTTCCAAGCCATGCTGTCAGGAAGACAGTTTAGCATAGACTCAGATCTCCTGGTTGATCTTTTCACTAGTTCTGT
GCAGATGAATCCCACAGATTACATCAATAATACAAAATCCAAGAATAAAGAATTAGAAACCTCCAAGAACAATGTAGTTC
AGCCAGCTTCAGAAGAGGGAAGAAAATCTAAATCCAAACCAGATAAGCAGCTTATCCAGTACACTGCTTTTCCACTTCTT
GCATTCCTCGATGGGAACCCTGCTTTCACTGTTGAACAGGACGGTACACCAGTATCATCAGAAGCTATGATCTCTGTAGA
TAAACCCATAGAAGTTGATGAGCTTCTGGATAGCAGCCTGGACCCAGAACCAACCCAGAGTAAGCTTGTTCGCCTGGAGC
CATTGACTGAAGCTGAAGCTAGGGAAGCTACACTGTTTTATTTATGTGAACTTGCTCCCGCACCTCTGGATAGTGATATG
CCACTTTTAAATAGCTAA

Alignment

ORF - retro_tbel_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.24 %
• Parental protein coverage: 90.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KYFKHNNMASFVRQLNMYGFRKVVHIDSGIVKQERDGPVEFQHPYFKQGQDDLLENIKRKVSSSKPEENK
          KY.KHNN..SFVRQLNM.GFRKVVH.DSGIVKQERDGPVEFQHPYFKQGQD.LLENIKRKVSSSKPEENK
Retrocopy KYLKHNNVVSFVRQLNMHGFRKVVHTDSGIVKQERDGPVEFQHPYFKQGQDELLENIKRKVSSSKPEENK

Parental  IRQEDLTKIISSAQKVQIKQETIESRLSELKSENESLWKEVSELRAKHAQQQQVIRKIVQFIVTLVQNNQ
          IRQEDLTKIISSAQKVQIKQETIESRLSELKSENESLWKEVSELRAKHAQ.Q.VIRKIVQFIVTLVQNNQ
Retrocopy IRQEDLTKIISSAQKVQIKQETIESRLSELKSENESLWKEVSELRAKHAQRQ-VIRKIVQFIVTLVQNNQ

Parental  LVSLKRKRPLLLNTNGAQKKNLFQHIVKEPTDNHHHKVPHSRTEGLKPRERISDDIIIYDVTDDNADEEN
          LVSLKRKR.LLLNTN.AQKKNLF.HIVKEPTDNHHHKVPHSRTEGL.PRE.ISDDIIIYDVTDDNADEEN
Retrocopy LVSLKRKRLLLLNTNRAQKKNLFRHIVKEPTDNHHHKVPHSRTEGLEPREWISDDIIIYDVTDDNADEEN

Parental  IPVIPETNEDVISDPSGCSQYPDIVIVEDDNEDEYAPVIQSGDQSEPARESLSSGSDCTSPLMSSAVQLN
          IPVIPETNEDVISDPS.CSQYPD.VIVEDD.EDEYAPVIQSGDQSEPARESLSSGSDCTSPLMSSA.QLN
Retrocopy IPVIPETNEDVISDPSSCSQYPDVVIVEDDYEDEYAPVIQSGDQSEPARESLSSGSDCTSPLMSSAIQLN

Parental  GSSSLTTEDPVTMMDSILNDNINLLGKVELLDYLDSIDCSLEDFQAMLSGRQFSIDPDLLVDLFTSSVQM
          GSSSLTTEDPVTMMDSILNDNINLLGKVELLDYLDSID.SLEDFQAMLSGRQFSID.DLLVDLFTSSVQM
Retrocopy GSSSLTTEDPVTMMDSILNDNINLLGKVELLDYLDSIDYSLEDFQAMLSGRQFSIDSDLLVDLFTSSVQM

Parental  NPTDYINNTKSENKGLETSKNNVVQPASEEGRKSKSKPDKQLIQYTAFPLLAFLDGNPASTVEQGGTPAS
          NPTDYINNTKS.NK.LETSKNNVVQPASEEGRKSKSKPDKQLIQYTAFPLLAFLDGNPA.TVEQ.GTP.S
Retrocopy NPTDYINNTKSKNKELETSKNNVVQPASEEGRKSKSKPDKQLIQYTAFPLLAFLDGNPAFTVEQDGTPVS

Parental  SEAMSSVDNPIEVDELLDSSLDPEPTQSKLVRLEPLTEAEASEATLFYLCELAPAPLDSDMPLLDS
          SEAM.SVD.PIEVDELLDSSLDPEPTQSKLVRLEPLTEAEA.EATLFYLCELAPAPLDSDMPLL.S
Retrocopy SEAMISVDKPIEVDELLDSSLDPEPTQSKLVRLEPLTEAEAREATLFYLCELAPAPLDSDMPLLNS

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_19 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_19 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,