RetrogeneDB ID: retro_tbel_3821

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_16844:66230..66890(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_tbel_3821
ATGAAGAGTGTGGCCTACAGTGCTTTTTCTCAGGAAGAGGCATAAGAGTTCGATGTTCAGCATGCAGAAGCCGAGCTGGC
CGAGGCCTTCTTGAAGGCCTTTCTGAAGCGCAGCGTACCCCGCATGAGCCAGCAAGCCCTGGAGGACCAGCTGCACTGCA
AGGCCCTTATTCTAGAGTACTTCATTCACCGGAAGAGATAGGAGAAGAAAAAGAAATCCAAAGGCCTCTCTTCCAGGCAG
AAGAGGGAACTGTGGCTCTTTGACATTAAGCCAGAGCAACAGAGATACAGTCTTTTTCTCCCACTGCATGAACTTTGGAA
GCAGTACATCTAGGACCTGTGCAATGGTCTCAAGCCAGACACGCAGCCACAGATGACTCAAGCCAAGCTGTTAAAGGCAG
ATCTTCATGGTGCTATTATTTCAGTCACAAAATCCAAATGCCCCTCGTATGTGGGTGTTACAGGAATTCTTCTACAGGAA
ACCAAGCACGTTTTCAAAATTATCACCAAAGAAGACTGCCTGAAAATTATCCCCAAGCTAAATTGTGTGTTCACTGTGGA
AATCGATGACTTTGTATCTTACATTTATGGGAGCAAATTCCAGCTTTGGTCAAGTGAGCGGTCTGAGATGAAGTTTAAAG
CAAAGGGCACAATCGCTCTC

Alignment

ORF - retro_tbel_3821 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSVVYRAFSQKEAKEFDVQHAGVARAEAFVKAFLKRSVPRMSQQALEDQLQRKAVILEYFTRRRKRKEK
          MKSV.Y.AFSQ.EA.EFDVQHA....AEAF.KAFLKRSVPRMSQQALEDQL..KA.ILEYF..R.KR.EK
Retrocopy MKSVAYSAFSQEEA*EFDVQHAEAELAEAFLKAFLKRSVPRMSQQALEDQLHCKALILEYFIHR-KR*EK

Parental  KKKSKGLSARQRRELRLFDIKPEQQRYSLFLPLHELWKQYIRDLCNGLKPDTQPQMIQAKLLKADLHGAI
          KKKSKGLS.RQ.REL.LFDIKPEQQRYSLFLPLHELWKQYI.DLCNGLKPDTQPQM.QAKLLKADLHGAI
Retrocopy KKKSKGLSSRQKRELWLFDIKPEQQRYSLFLPLHELWKQYI*DLCNGLKPDTQPQMTQAKLLKADLHGAI

Parental  ISVTKSKCPSYVGVTGILLQETKHVFKIITKEDRLKVIPKLNCVFTVEIDDFVSYIYGSKFQLRSSERSA
          ISVTKSKCPSYVGVTGILLQETKHVFKIITKED.LK.IPKLNCVFTVEIDDFVSYIYGSKFQL.SSERS.
Retrocopy ISVTKSKCPSYVGVTGILLQETKHVFKIITKEDCLKIIPKLNCVFTVEIDDFVSYIYGSKFQLWSSERSE

Parental  KKFKAKGTIDL
          .KFKAKGTI.L
Retrocopy MKFKAKGTIAL

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_3821 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3821 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,