RetrogeneDB ID: retro_ogar_2557

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873634.1:5844910..5845574(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000032067
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000009152
• Aliases: None
• Description: None

Sequence

>retro_ogar_2557
ACTGACAAGCCCTTGCGTCTGCCTTTGTGAGATGTTTACAAAATTGGTGGTATCAGTACTGCCCCTGTGGCCCAAGTGGA
AGTTGGTGTTCTCAACTCTGGCATGGTGGTCACCTTTGCTCCAGTTAATGATATAACTGAAGTAAAGTCTGTTGAAATGC
ACCATGAAGATTTGAGCAAATCTCTTCCAGGGCACAACATGGGCTTCAACGTCAGAATGTGTCTGCCAAAGATGTTCGTC
GTGGCAACGCTGCTGTTGATAGCAAAATGACCCAAGGATGGAAGCAGCTGGCTTCACTGCCCAGGTGGTTATCCTGAACC
ATCCAGGCCAAATTAGTGCTGGTTGTGCTCCTGTACTGGACTGTCACACACCTCACGTTGCTTGTAAGTTTGCTGAGCTG
AAGGAACAGATTGACTGCTGCTCTGGTAAGAAGCTGGAAAATGGCCCTAAATTCCTGAAATCTGGCGATGCTACCATCAT
CAATATGTTTCCTGGCAAACCAATGTATATTGAGAGCTTCTCAGACTATCCTCCTCTGGGTCCTTTCACTGTTCGTGACA
TGAGACAGACACCCTTTGCTGTGGGTATCATCAAAGCAGTGGACAAGAAGGCTGCTGGAGCTGGCAAGGTCACTAAGTCT
GCCCAGAAAGCTCAGAAGGCTAAA

Alignment

ORF - retro_ogar_2557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.7 %
• Parental protein coverage: 62.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFN
          TDKPLRLPL.DVYKIGGI.T.PV..VE.GVL..GMVVTFAPVN..TEVKSVEMHHE.LS..LPG.N.GFN
Retrocopy TDKPLRLPL*DVYKIGGISTAPVAQVEVGVLNSGMVVTFAPVNDITEVKSVEMHHEDLSKSLPGHNMGFN

Parental  VK-NVSVKDVRRGNVAGDSK-NDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFAELKEKI
          V..NVS.KDVRRGN.A.DSK.NDP.MEAAGFTAQV.ILNHPGQISAG.APVLDCHT.H.ACKFAELKE.I
Retrocopy VR<NVSAKDVRRGNAAVDSK<NDPRMEAAGFTAQVVILNHPGQISAGCAPVLDCHTPHVACKFAELKEQI

Parental  DRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPPLGRFAVRDMRQT-VAVGVIKAVDKKAAGA
          D..SGKKLE.GPKFLKSGDA.I..M.PGKPM..ESFSDYPPLG.F.VRDMRQT..AVG.IKAVDKKAAGA
Retrocopy DCCSGKKLENGPKFLKSGDATIINMFPGKPMYIESFSDYPPLGPFTVRDMRQTPFAVGIIKAVDKKAAGA

Parental  GKVTKSAQKAQKAK
          GKVTKSAQKAQKAK
Retrocopy GKVTKSAQKAQKAK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2557 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 15 parental genes, and 136 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Echinops telfairi	ENSETEG00000004236	14 retrocopies	retro_etel_1189, retro_etel_1248, retro_etel_1260, retro_etel_1429, retro_etel_1436, retro_etel_1472, retro_etel_1578, retro_etel_1602, retro_etel_1682, retro_etel_1808, retro_etel_2135, retro_etel_366, retro_etel_411, retro_etel_830,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Microcebus murinus	ENSMICG00000015319	21 retrocopies	retro_mmur_1027, retro_mmur_1116, retro_mmur_1145, retro_mmur_1182, retro_mmur_1190, retro_mmur_12, retro_mmur_1282, retro_mmur_1316, retro_mmur_1339, retro_mmur_1343, retro_mmur_1350, retro_mmur_1568, retro_mmur_171, retro_mmur_26, retro_mmur_273, retro_mmur_49, retro_mmur_682, retro_mmur_729, retro_mmur_825, retro_mmur_877, retro_mmur_9,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Otolemur garnettii	ENSOGAG00000004630	8 retrocopies	retro_ogar_1067, retro_ogar_2034, retro_ogar_2329, retro_ogar_2497, retro_ogar_2583, retro_ogar_3191, retro_ogar_3270, retro_ogar_643,
Otolemur garnettii	ENSOGAG00000009152	10 retrocopies	retro_ogar_1215, retro_ogar_1622, retro_ogar_1779, retro_ogar_1840, retro_ogar_2281, retro_ogar_2526, retro_ogar_2557 , retro_ogar_3013, retro_ogar_3046, retro_ogar_3271,
Pongo abelii	ENSPPYG00000016777	1 retrocopy	retro_pabe_12,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Tupaia belangeri	ENSTBEG00000012151	51 retrocopies	retro_tbel_1084, retro_tbel_1330, retro_tbel_1373, retro_tbel_1452, retro_tbel_166, retro_tbel_1841, retro_tbel_1969, retro_tbel_1994, retro_tbel_2088, retro_tbel_2091, retro_tbel_2179, retro_tbel_2205, retro_tbel_2206, retro_tbel_2218, retro_tbel_2232, retro_tbel_2419, retro_tbel_2505, retro_tbel_259, retro_tbel_2627, retro_tbel_2718, retro_tbel_2738, retro_tbel_2758, retro_tbel_282, retro_tbel_2976, retro_tbel_3032, retro_tbel_3065, retro_tbel_3067, retro_tbel_3281, retro_tbel_3307, retro_tbel_3315, retro_tbel_338, retro_tbel_354, retro_tbel_360, retro_tbel_372, retro_tbel_3813, retro_tbel_3865, retro_tbel_3967, retro_tbel_4125, retro_tbel_4192, retro_tbel_4282, retro_tbel_4352, retro_tbel_4370, retro_tbel_4466, retro_tbel_4496, retro_tbel_4639, retro_tbel_4660, retro_tbel_4695, retro_tbel_473, retro_tbel_588, retro_tbel_620, retro_tbel_903,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,