RetrogeneDB ID: retro_tbel_4608

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_92922:2112..2729(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FGFR1OP2
• Ensembl ID: ENSTBEG00000011581
• Aliases: None
• Description: FGFR1 oncogene partner 2 [Source:HGNC Symbol;Acc:23098]

Sequence

>retro_tbel_4608
ATGAGTTGCACAATTGAGAAGGCACTTGCTGTTGCTAAAGTGCTTGTTGAAAGGTTTAGAGATCAGAATGATGCAGTAGA
ATCTCTGATAGAGCAAACCACAGCTCTCAACATACAAGTGGAAGCAATGAATCAGTATCAGAAAAAATTTCAAGAACTTG
ATGAAGTTACAAGACATCGGCCATGGTCCACATTAGTTATGAGAATCCAGCAAGAAAACAGACAAATAAGAATATTACAA
AAAGAGAACAAAGAATTACTAACATCACTGGAAAACATCAGTCTACCTTGGCACTTATAATGAGTAAGTATTGAGATCAA
ATGTTTATATTGCTAATGGCCAAGAAAAAATATGCTCTGGGTATAATAATAAAAGTTTGACGCTCCAAGATTGATATGTT
GCACCATAACAACTTCAAAGGATTCTCTCTTGATGTATCTTGACACATCCTTGAAGAACCTCAATGTGAACTGGAGAGGA
GGCACTTGGAAGTAAATCATAATGATTTACAAGCACAAGTTGACTAGATAACTCAAATGGCAATAGTTATGAGAAAAGTC
ATTGAAATTGATGAACAACAAGGCTGCAAGAAACAGAAATGAATATTTCAACTTGAA

Alignment

ORF - retro_tbel_4608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSCTIEKALADAKALVERLRDHDDAAESLIEQTTALNKRVEAMKQYQEE-SELNEVARHRPRSTLVMGIX
          MSCTIEKALA.AK.LVER.RD..DA.ESLIEQTTALN..VEAM.QYQ....EL.EV.RHRP.STLVM.I.
Retrocopy MSCTIEKALAVAKVLVERFRDQNDAVESLIEQTTALNIQVEAMNQYQKKFQELDEVTRHRPWSTLVMRIQ

Parental  XXXXXXXXXXXXXXXLRTSLE-EHQSALELIMSKYREQMFRLLMASKKDDPGIIMKLKEQHSKXXXXXXX
          ...............L.TSLE..HQS.L.LIMSKY..QMF.LLMA.KK...GII...K...SK.......
Retrocopy QENRQIRILQKENKELLTSLE<KHQSTLALIMSKY*DQMFILLMAKKKYALGII--IKV*RSKIDMLHHN

Parental  XXXXXXXXASRHILEAPQHVLERRHLEANQNELQAHVDQITEMAAVMRKAIEIDEQQGCKEQERIFQLE
          .........S.HILE.PQ..LERRHLE.N.N.LQA.VD.IT.MA.VMRK.IEIDEQQGCK.Q..IFQLE
Retrocopy NFKGFSLDVS*HILEEPQCELERRHLEVNHNDLQAQVD*ITQMAIVMRKVIEIDEQQGCKKQK*IFQLE

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_4608 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4608 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006966	2 retrocopies	retro_dnov_2342, retro_dnov_2594,
Equus caballus	ENSECAG00000016890	1 retrocopy	retro_ecab_988,
Homo sapiens	ENSG00000111790	1 retrocopy	retro_hsap_994,
Loxodonta africana	ENSLAFG00000012476	1 retrocopy	retro_lafr_486,
Monodelphis domestica	ENSMODG00000016618	2 retrocopies	retro_mdom_1788, retro_mdom_244,
Mus musculus	ENSMUSG00000040242	2 retrocopies	retro_mmus_3669, retro_mmus_720,
Pongo abelii	ENSPPYG00000004375	1 retrocopy	retro_pabe_839,
Pan troglodytes	ENSPTRG00000004783	1 retrocopy	retro_ptro_756,
Tupaia belangeri	ENSTBEG00000007772	1 retrocopy	retro_tbel_2455,
Tupaia belangeri	ENSTBEG00000011581	2 retrocopies	retro_tbel_3732, retro_tbel_4608 ,