RetrogeneDB ID: retro_tbel_3246

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_134831:9578..10277(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFAP1
• Ensembl ID: ENSTBEG00000005050
• Aliases: None
• Description: microfibrillar-associated protein 1 [Source:HGNC Symbol;Acc:7032]

Sequence

>retro_tbel_3246
AAGCAAAATGACAGATGTCTACTACTAGAATCAACTTATGAAATAGAAAGACCTCAGAAGGGGCTGCAGCAGGAAGCAGA
GTTCACAGCCAAGGAGAGGTGCAGGTACATGCTCCAGGTCCTAGAAAAGGCCATGAAAAAGCTGGAGACTGGGTGGCCCT
TGGCTGCACGGGATGCTCTCAATGGAGATGATGAAAATGAGGAGGAGGTATATGAGGCATGGGAAGTCTGAGAACTAAAA
AGAATCGAGAGAGAGAGAGGAGATCGAGAAGCACTTGAGGAAAAGAAAGCAGAAATGTAACACTTGCAGAACCTGACTGA
GGAGGAGAGGCGGGCCCAGCTCCAGGCAAATGTCACAGTCATCACAAACCAAGATGTGAAGGGCAAGTGCAGGTTTTTAC
AGAAGTACTATCACTGGGGTACCCTCTTCATGGACAAAGAGGAAGACGTATACAAGAGAGATTTCAGCGTGCCTACCCTA
GAGGACCATTTCGACAAAATTGTTCTTCCTAAAGTCATACAGGTCAAGAACTTTGTTTGCTCTGGCTGGACCAAATACAC
TCACCTGGTTGATCAAGACACCACCTCCTTCGACTCAGCGTGGGGCCAAGAGAGTGCCCCAAACAGAAAGTTCTTTAAAG
AAAAGGCAGCTGGGGTGCAAGATGTGTTTGAACGACCATCTGCCAAGAAGCAGAGAACT

Alignment

ORF - retro_tbel_3246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.83 %
• Parental protein coverage: 69.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKKDRVTVQEREAEALK-QKELEQEAKRMAEERRKYTLKIVEEETKKELEENKRSLAALDALNTDDENDE
          ...DR....E...E....QK.L.QEA...A.ER..Y.L...E...KK...E....LAA.DALN.DDEN.E
Retrocopy KQNDRCLLLESTYEIERPQKGLQQEAEFTAKERCRYMLQVLEKAMKKL--ETGWPLAARDALNGDDENEE

Parental  EEYEAWKVRELKRIKRDREDREALEKEKAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKFLQKYYH
          E.YEAW.V.ELKRI........ALE..KAE.....NLTEEERRA.L.AN..VITN..VKGK..FLQKYYH
Retrocopy EVYEAWEV*ELKRIXXXXXXXXALEEKKAEM*HLQNLTEEERRAQLQANVTVITNQDVKGKCRFLQKYYH

Parental  RGAFFMDEDEEVYKRDFSAPTLEDHFNKTILPKVMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGQESAQN
          .G..FMD..E.VYKRDFS.PTLEDHF.K..LPKV.QVKNF..SG.TKYTHLVDQDTTSFDSAWGQESA.N
Retrocopy WGTLFMDKEEDVYKRDFSVPTLEDHFDKIVLPKVIQVKNFVCSGWTKYTHLVDQDTTSFDSAWGQESAPN

Parental  TKFFKQKAAGVRDVFERPSAKKRKT
          .KFFK.KAAGV.DVFERPSAKK..T
Retrocopy RKFFKEKAAGVQDVFERPSAKKQRT

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_3246 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3246 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013870	1 retrocopy	retro_dord_22,
Myotis lucifugus	ENSMLUG00000013000	2 retrocopies	retro_mluc_1384, retro_mluc_2298,
Mus musculus	ENSMUSG00000048222	2 retrocopies	retro_mmus_1147, retro_mmus_2346,
Mus musculus	ENSMUSG00000068479	2 retrocopies	retro_mmus_2386, retro_mmus_2638,
Otolemur garnettii	ENSOGAG00000010206	1 retrocopy	retro_ogar_1784,
Rattus norvegicus	ENSRNOG00000015984	1 retrocopy	retro_rnor_83,
Sarcophilus harrisii	ENSSHAG00000014628	1 retrocopy	retro_shar_107,
Ictidomys tridecemlineatus	ENSSTOG00000006967	2 retrocopies	retro_itri_1105, retro_itri_1494,
Tupaia belangeri	ENSTBEG00000005050	2 retrocopies	retro_tbel_3001, retro_tbel_3246 ,