RetrogeneDB ID: retro_tbel_1225

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4147:277435..278093(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000003716
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000002194
• Aliases: None
• Description: None

Sequence

>retro_tbel_1225
ATGAAGAGTGTGGTCTATTGTGCTTTTTCTCAGAAAGAAGCAAAAGAGTTTGATGTTCAGCATGCAGGAGTCATGCAGGC
CGAGGCCTTCGTGAAGGCCTTCCTGAAGCGCAGTGTGCCCCGCATGAGCCAGCAAGCCGTGGAGGACCAGCTGCAGCTCA
AGGCCGTTATTCTAGAGTACTTCACTCGCTGGAGGAGAAAGGACAAGAAAAAGAAATCCAGAGGCCTCTCTGCCAGGCAG
AGGAGGGAACTGCGGCTCTTTGACATTAAGGCAGAGCAACAGAGATAGTCTTTTTCTCCTGCTGCTTGAACTTTGGAAGC
AGTACATCCGGGACCTGTGCAATGGTCTCAAGCCCGACATGCAGTCACAGATGATTCGAGCCAAGTTGTTAAAGGCAGAT
CTTCATGGTGCTATTATTTCAGGCACAAAATCCAAATGCCCCTCGTATGTGAGTGTGACAGAAATTCTTCTACAGGAAAC
CAAGCACGTTTTCAAAATTATCACCAAAGAAGACCGCCTGAAAGTTATCCTCAAGCTAAATTGTGTGTTAACTGTGGAAA
TCGATGACTTTGTATCCTACATTTATGGGAGCAAATTCCAGCTTCGGTCAAGTGAGCGGTCTCCAAAGAAGTTTAAAGCA
AAGGGCACAATCGACCTT

Alignment

ORF - retro_tbel_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKSVVYRAFSQKEAKEFDVQHAGVARAEAFVKAFLKRSVPRMSQQALEDQLQRKAVILEYFTRRRKRKEK
          MKSVVY.AFSQKEAKEFDVQHAGV..AEAFVKAFLKRSVPRMSQQA.EDQLQ.KAVILEYFTR.R.RK.K
Retrocopy MKSVVYCAFSQKEAKEFDVQHAGVMQAEAFVKAFLKRSVPRMSQQAVEDQLQLKAVILEYFTRWR-RKDK

Parental  KKKSKGLSARQRRELRLFDIKPEQQRYSLFLP-LHELWKQYIRDLCNGLKPDTQPQMIQAKLLKADLHGA
          KKKS.GLSARQRRELRLFDIK.EQQR.S.F.P.L.ELWKQYIRDLCNGLKPD.Q.QMI.AKLLKADLHGA
Retrocopy KKKSRGLSARQRRELRLFDIKAEQQR*S-FSP>LLELWKQYIRDLCNGLKPDMQSQMIRAKLLKADLHGA

Parental  IISVTKSKCPSYVGVTGILLQETKHVFKIITKEDRLKVIPKLNCVFTVEIDDFVSYIYGSKFQLRSSERS
          IIS.TKSKCPSYV.VT.ILLQETKHVFKIITKEDRLKVI.KLNCV.TVEIDDFVSYIYGSKFQLRSSERS
Retrocopy IISGTKSKCPSYVSVTEILLQETKHVFKIITKEDRLKVILKLNCVLTVEIDDFVSYIYGSKFQLRSSERS

Parental  AKKFKAKGTIDL
          .KKFKAKGTIDL
Retrocopy PKKFKAKGTIDL

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_1225 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1225 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000008041	1 retrocopy	retro_mputfur_1088,
Oryctolagus cuniculus	ENSOCUG00000015974	1 retrocopy	retro_ocun_1367,
Otolemur garnettii	ENSOGAG00000011168	2 retrocopies	retro_ogar_3293, retro_ogar_541,
Sorex araneus	ENSSARG00000004748	1 retrocopy	retro_sara_410,
Tupaia belangeri	ENSTBEG00000002194	6 retrocopies	retro_tbel_1225 , retro_tbel_1516, retro_tbel_2043, retro_tbel_3671, retro_tbel_3821, retro_tbel_89,