RetrogeneDB ID: retro_tbel_4058

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_61040:636..905(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000016085
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000016632
• Aliases: None
• Description: None

Sequence

>retro_tbel_4058
ATGCCCAAGATGAAGGCTGAAGGGGAGGCTAAAGGAGATACAGCCGAGGTGAAGAACGGACCACAGAGAAGATGTGCAAG
GTTGTCTGCAAAACCTGCTCCTCCACAGCCAGAGCCCAAGCCTAAAAATCCCCTGCAAAGAAGGGAGAGAAGGTGCCCAA
AGGAAAAAAGGGAAAAGGTGATGCTGGCAAGGATGGGAACAACCCTGCAGAAAACGGAGATGCCAAAACAGCCCAGGCAC
AGAAAGCTGAAGGTGCTGGAGATGCCGAG

Alignment

ORF - retro_tbel_4058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPK-KAPAKKGEKVPKGKKGKADAGKDGNNP
          MPK.KAEG.AKGD.A.VK..PQRR.ARLSAKPAPP.PEPKPK.K.PAKKGEKVPKGKKGK.DAGKDGNNP
Retrocopy MPKMKAEGEAKGDTAEVKNGPQRRCARLSAKPAPPQPEPKPK<KSPAKKGEKVPKGKKGKGDAGKDGNNP

Parental  AENGDAKTDQXXKAEGAGDAE
          AENGDAKT.Q..KAEGAGDAE
Retrocopy AENGDAKTAQAQKAEGAGDAE

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_4058 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4058 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 12 parental genes, and 138 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038104	7 retrocopies	retro_btau_1041, retro_btau_1160, retro_btau_1200, retro_btau_1292, retro_btau_1297, retro_btau_1684, retro_btau_482,
Canis familiaris	ENSCAFG00000023168	35 retrocopies	retro_cfam_1043, retro_cfam_1188, retro_cfam_1314, retro_cfam_1360, retro_cfam_1519, retro_cfam_1546, retro_cfam_1593, retro_cfam_1606, retro_cfam_1629, retro_cfam_1681, retro_cfam_1708, retro_cfam_1784, retro_cfam_1989, retro_cfam_2060, retro_cfam_2097, retro_cfam_2133, retro_cfam_266, retro_cfam_317, retro_cfam_324, retro_cfam_351, retro_cfam_353, retro_cfam_38, retro_cfam_381, retro_cfam_410, retro_cfam_446, retro_cfam_538, retro_cfam_623, retro_cfam_628, retro_cfam_705, retro_cfam_745, retro_cfam_783, retro_cfam_795, retro_cfam_821, retro_cfam_845, retro_cfam_860,
Echinops telfairi	ENSETEG00000013571	33 retrocopies	retro_etel_1035, retro_etel_1097, retro_etel_1210, retro_etel_1253, retro_etel_1282, retro_etel_1298, retro_etel_1314, retro_etel_1346, retro_etel_1398, retro_etel_1582, retro_etel_165, retro_etel_1690, retro_etel_1710, retro_etel_178, retro_etel_1836, retro_etel_1845, retro_etel_1939, retro_etel_1945, retro_etel_1951, retro_etel_1961, retro_etel_2079, retro_etel_253, retro_etel_292, retro_etel_298, retro_etel_446, retro_etel_481, retro_etel_505, retro_etel_511, retro_etel_571, retro_etel_61, retro_etel_768, retro_etel_819, retro_etel_881,
Felis catus	ENSFCAG00000012812	3 retrocopies	retro_fcat_1842, retro_fcat_4, retro_fcat_530,
Macropus eugenii	ENSMEUG00000010966	8 retrocopies	retro_meug_1178, retro_meug_126, retro_meug_1859, retro_meug_1910, retro_meug_1997, retro_meug_248, retro_meug_369, retro_meug_76,
Mus musculus	ENSMUSG00000003038	2 retrocopies	retro_mmus_202, retro_mmus_2582,
Pteropus vampyrus	ENSPVAG00000017269	5 retrocopies	retro_pvam_1046, retro_pvam_1059, retro_pvam_1065, retro_pvam_379, retro_pvam_4,
Sorex araneus	ENSSARG00000013139	3 retrocopies	retro_sara_12, retro_sara_17, retro_sara_176,
Sus scrofa	ENSSSCG00000003555	3 retrocopies	retro_sscr_573, retro_sscr_66, retro_sscr_985,
Tupaia belangeri	ENSTBEG00000016632	33 retrocopies	retro_tbel_1351, retro_tbel_16, retro_tbel_1844, retro_tbel_21, retro_tbel_2219, retro_tbel_2498, retro_tbel_2670, retro_tbel_3050, retro_tbel_309, retro_tbel_3101, retro_tbel_3112, retro_tbel_3121, retro_tbel_3149, retro_tbel_320, retro_tbel_3413, retro_tbel_3462, retro_tbel_36, retro_tbel_389, retro_tbel_4058 , retro_tbel_417, retro_tbel_4469, retro_tbel_448, retro_tbel_4615, retro_tbel_4644, retro_tbel_475, retro_tbel_50, retro_tbel_538, retro_tbel_62, retro_tbel_65, retro_tbel_66, retro_tbel_704, retro_tbel_732, retro_tbel_757,
Tursiops truncatus	ENSTTRG00000005681	5 retrocopies	retro_ttru_1392, retro_ttru_1443, retro_ttru_3, retro_ttru_345, retro_ttru_788,
Vicugna pacos	ENSVPAG00000008076	1 retrocopy	retro_vpac_183,