RetrogeneDB ID: retro_tbel_1943

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_6050:289250..289634(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000006941
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSTBEG00000009218
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_tbel_1943
TTCAATGTGGAGACTGGAGAGGACCAGAACGTTGATTTCGCTGTCTGGTACGTGGGTGCCCAGGCCCAGACCCTCCTCTG
TGGCTCACTATTTCCAGAATACACAAGGCTAATCTTTGTGGGGGAAAGCAATGACAGAGAGCGTTTGAAGGAGGCCCGTG
AGATATCATGAGGGTGCTGTCTGAAGAAGTTCTCAGGGGGACCGTCCTCCTGTGTTTCCCAGTAAGCAAGACCTTCCAAA
GCACAGATGTGGCCGGAACCTCTCAGAAGCTGGGGCTGCACTCTCTGCACACAGGAACTGGTACCTTCAGGCCACCTGCG
CCATCAGTCAGGACCGGGTCTACCAGGACTGGGCTGGCTGTCCAATCAGCTGCGGAGCCAGAAG

Alignment

ORF - retro_tbel_1943 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.39 %
• Parental protein coverage: 72.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  FNVETVEYKNISFTVWDVGGQDKIR-PLW-RHYFQNTQG-LIFVVDSNDRERVNEARE-ELMRMLAEDEL
          FNVET.E..N..F.VW.VG.Q.....PLW..HYFQNTQG.LIFV..SNDRER..EARE...MR.L.E..L
Retrocopy FNVETGEDQNVDFAVWYVGAQAQTL<PLW<AHYFQNTQG<LIFVGESNDRERLKEARE<DIMRVLSEEVL

Parental  RDAVLLVFANKQDLPNAMNAAEITDKLGLHSLR-HRNWYIQATCATSGDGLYE-GLDWLSNQLRNQK
          R..VLL.F............A....KLGLHSL..HRNWY.QATCA.S.D..Y..GL.WLSNQLR.QK
Retrocopy RGTVLLCFPVSKTFQST-DVAGTSQKLGLHSLH<HRNWYLQATCAISQDRVYQ<GLGWLSNQLRSQK

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_1943 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1943 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 16 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Cavia porcellus	ENSCPOG00000021174	1 retrocopy	retro_cpor_1310,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Felis catus	ENSFCAG00000029374	1 retrocopy	retro_fcat_1829,
Homo sapiens	ENSG00000143761	3 retrocopies	retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Gorilla gorilla	ENSGGOG00000011263	5 retrocopies	retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Mus musculus	ENSMUSG00000048076	1 retrocopy	retro_mmus_1718,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Tupaia belangeri	ENSTBEG00000007415	1 retrocopy	retro_tbel_2075,
Tupaia belangeri	ENSTBEG00000009218	9 retrocopies	retro_tbel_1943 , retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000014186	2 retrocopies	retro_ttru_1679, retro_ttru_347,