RetrogeneDB ID: retro_tbel_2276

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_108368:592..1117(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA4
• Ensembl ID: ENSTBEG00000009268
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 4 [Source:HGNC Symbol;Acc:14885]

Sequence

>retro_tbel_2276
CATCAGCTGTCAGTACCTTAGATTTATATAGTAGTGCACAAGAAAACGGGCCCTGCAAAACAATGTGATTTGTGACAAGT
GTGAAGCTGAGGGGTGAGAAGGAGCAGCAGAGTGCTGTCCCAATTGCTGAGGTACTGGAATGTAAGTAAGAATTCATCAG
ATAGGACCTGGAATGGTTCAGCAAATTCAGTCTGTATGCAAGGCCATGGGGAGTGGATCAGTCCTAAAGACAGATGTAAA
AGTTGCAACGGAAGGAAGATAGTTCAAGAGAAGAAGAGTCTAGAAGTTCATGTTGACAAAGGCATGAAAGATGGCCAGAA
GATAACATTCCATGGTGGAGGAGACCAAGAACCAGGACTGGAGCCAGGAGATGTTATCATTATATTAAATCAGAAAGATC
ATGCTGTTGTTACTAGGTGAGGAGAGGACCTTTTCATGTGTGTGGTCATACAGCTGGTTGAAGCATTGCATGGCTTCCAG
AAGCCAATTTCCAGTCTTGACGACTGAACCATAGTCATCACCTCT

Alignment

ORF - retro_tbel_2276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.59 %
• Parental protein coverage: 72.87 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HQLSV-TLEDLYNGV-TKKLALQKNVICEKCEGVGGKKGSVEKCPLCKGRGMQVHIQHIGPGMVQQIQTV
          HQLSV.TL.DLY....T.K.ALQ.NVIC.KCE..G...G..E.CP.C.G.GM.V.I..IGPGMVQQIQ.V
Retrocopy HQLSV<TL-DLYSSA<TRKRALQNNVICDKCEAEG*E-GAAECCPNC*GTGM*VRIHQIGPGMVQQIQSV

Parental  CIECK-GQGERINPKDRCETCSGAKVIREKKIIEVHVEKGMKDGQKILFHEG-DQEPELEPGDVIIVLDQ
          ...CK.G.GE.I.PKDRC..C.G.K...EKK..EVHV.KGMKDGQKI.FH.G.DQEP.LEPGDVII.L.Q
Retrocopy ---CK<GHGEWISPKDRCKSCNGRKIVQEKKSLEVHVDKGMKDGQKITFHGGGDQEPGLEPGDVIIILNQ

Parental  KDHSVFQRRGHDLIMKMKIQLSEALCGFKKTIKTLDDRILVITS
          KDH.V..R.G.DL.M...IQL.EAL.GF.K.I..LDD...VITS
Retrocopy KDHAVVTR*GEDLFMCVVIQLVEALHGFQKPISSLDD*TIVITS

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_2276 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2276 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 11 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012576	1 retrocopy	retro_amel_1659,
Dipodomys ordii	ENSDORG00000005972	4 retrocopies	retro_dord_245, retro_dord_280, retro_dord_333, retro_dord_533,
Echinops telfairi	ENSETEG00000004320	4 retrocopies	retro_etel_1010, retro_etel_1031, retro_etel_1067, retro_etel_608,
Macropus eugenii	ENSMEUG00000015982	4 retrocopies	retro_meug_1059, retro_meug_1893, retro_meug_292, retro_meug_624,
Microcebus murinus	ENSMICG00000008789	6 retrocopies	retro_mmur_1242, retro_mmur_1460, retro_mmur_39, retro_mmur_482, retro_mmur_496, retro_mmur_578,
Mus musculus	ENSMUSG00000032285	1 retrocopy	retro_mmus_2632,
Otolemur garnettii	ENSOGAG00000006752	5 retrocopies	retro_ogar_1760, retro_ogar_1985, retro_ogar_221, retro_ogar_2656, retro_ogar_841,
Ochotona princeps	ENSOPRG00000007594	1 retrocopy	retro_opri_1028,
Tupaia belangeri	ENSTBEG00000000596	23 retrocopies	retro_tbel_1281, retro_tbel_134, retro_tbel_1529, retro_tbel_1542, retro_tbel_2260, retro_tbel_2293, retro_tbel_2316, retro_tbel_2428, retro_tbel_2445, retro_tbel_2917, retro_tbel_2965, retro_tbel_2972, retro_tbel_329, retro_tbel_3345, retro_tbel_3353, retro_tbel_3692, retro_tbel_4014, retro_tbel_4223, retro_tbel_432, retro_tbel_591, retro_tbel_617, retro_tbel_634, retro_tbel_842,
Tupaia belangeri	ENSTBEG00000009268	9 retrocopies	retro_tbel_2276 , retro_tbel_2308, retro_tbel_2790, retro_tbel_2831, retro_tbel_3242, retro_tbel_4322, retro_tbel_4735, retro_tbel_772, retro_tbel_796,
Tarsius syrichta	ENSTSYG00000008600	1 retrocopy	retro_tsyr_1752,