RetrogeneDB ID: retro_tbel_4110

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_67680:4023..4701(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EAF2
• Ensembl ID: ENSTBEG00000017542
• Aliases: None
• Description: ELL associated factor 2 [Source:HGNC Symbol;Acc:23115]

Sequence

>retro_tbel_4110
GACTTCAAACCTGCTTCTATTGATACTTCTTGTGAAGGAGATCTTGAGGTTGGCAAAGGTGAACAGGTGACAATAACTCT
ACCAAACTTAGAAGGTTCAACAACGCCAGTAACCGTTTTCAAAGGTTCAAAGAAACCTTACTTAAGAGAATGCATTTTGA
TTATTAACCGTGATACTGGAGAATGCCGACTAGAAAAACTCAGCAGCAATATCACAGTAAAGAAAACAAGAGTTGAAGGA
AGCAGTGCAATTCAGTATTGTTTAGAGCAGCAGCAACAACAAATGCGGAACCCAACCAGGACTCCATATCTTCCAAAACA
TTCTATATCCGAAGACAAGATGTCTCCAGCATCTCCAATGGATGACATTGAAAGAGAACTGAAGGCAGAAGCCAGTTTAA
TGGATCAGATGAGTAATTGGGAGAGTTCCTCAGATTCCAAAAGTCCATCATCTTCAAGTAGCGAGGATAGTTCTAGTGAC
TCAGAAGATGAAGAGTACAGATCCTCTCCTGATTCAGAGAATTATACCTCAGGACATCCCACCATGTCTGCCATGCCACA
GTACAGGAGTCCTGAGATAGATCCCAGTCCTAATAGATTTCATGTCAACAGTGACCTTCTTATGAATACTCTATGAAATG
ATTTGCAACTGAGTGACTCAGGAAGTGACAGTGATGAC

Alignment

ORF - retro_tbel_4110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.36 %
• Parental protein coverage: 86.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFKPASIDTSCEGDLEVGKGEQVTITLPNLEGSTTPVTV-KGSKKPYLRECILIINHDTGECRLEKLSSN
          DFKPASIDTSCEGDLEVGKGEQVTITLPNLEGSTTPVTV.KGSKKPYLRECILIIN.DTGECRLEKLSSN
Retrocopy DFKPASIDTSCEGDLEVGKGEQVTITLPNLEGSTTPVTVFKGSKKPYLRECILIINRDTGECRLEKLSSN

Parental  ITVKKTRVEGSSKIQYRLEQQQQQMRNPTRTPYLPKHSTSEDKMSPASPMDDIERELKAEASLMDQMSSC
          ITVKKTRVEGSS.IQY.LEQQQQQMRNPTRTPYLPKHS.SEDKMSPASPMDDIERELKAEASLMDQMS..
Retrocopy ITVKKTRVEGSSAIQYCLEQQQQQMRNPTRTPYLPKHSISEDKMSPASPMDDIERELKAEASLMDQMSNW

Parental  ESSSDSKSSSSSSSEDSSSDSEDEECRSSPDSGNYTSGHPTMSAMP-CRSPEIDPSPNRFHDNSGLLMNT
          ESSSDSKS.SSSSSEDSSSDSEDEE.RSSPDS.NYTSGHPTMSAMP..RSPEIDPSPNRFH.NS.LLMNT
Retrocopy ESSSDSKSPSSSSSEDSSSDSEDEEYRSSPDSENYTSGHPTMSAMPQYRSPEIDPSPNRFHVNSDLLMNT

Parental  LRNDLQLSDSGSDSDD
          L.NDLQLSDSGSDSDD
Retrocopy L*NDLQLSDSGSDSDD

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_4110 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4110 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006427	1 retrocopy	retro_cpor_235,
Felis catus	ENSFCAG00000018226	1 retrocopy	retro_fcat_1398,
Macropus eugenii	ENSMEUG00000005416	1 retrocopy	retro_meug_1621,
Monodelphis domestica	ENSMODG00000018271	1 retrocopy	retro_mdom_25,
Tupaia belangeri	ENSTBEG00000017542	1 retrocopy	retro_tbel_4110 ,