RetrogeneDB ID: retro_ggor_1401

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:18799662..18800038(-)
• Located in intron of: ENSGGOG00000012718

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL34
• Ensembl ID: ENSGGOG00000007650
• Aliases: None
• Description: None

Sequence

>retro_ggor_1401
CTCTTCCAGGGATGCTATCTAGAGGCACTCAGCATGATCCAGTGTTTGATGCACCATCATAGGCTTTTCTACAACACAGC
ATCTAACAAAACTAGGCTGTCCCAAACCCTGGTATTGTTTACCTTTATATCAAGAAGGTAGGGAAAGCACCAATGTCTGC
ATGTGGCGTGTGCCCAGGCAGACTTCAAGGGATTTATGCTGTGAGACCTCAAGTTCTTGTGAGGTTGTCTAAAATTTTAA
AAAGTGTCAGCACGACCAATGGTGTTTCCATGACTGCTAAATGTATCCACGACAGGACCAAGCATGCTTTCCTTTCAAAG
AGCAGAATGTCATCGTGAAAATGTTGAAGGCACAAGCCCAGAGTCAGAAAGCTAAA

Alignment

ORF - retro_ggor_1401 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.69 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFRGRCLQALRMVQRLTYRRRLSYNTASNKTRLSRT-PGNRIVYLYTKKVGKAPKSACGVCPGRLRGVRA
          LF.G..L.AL.M.Q.L....RL.YNTASNKTRLS.T.PG..IVYLY.KKVGKAP.SACGVCPGRL.G..A
Retrocopy LFQGCYLEALSMIQCLMHHHRLFYNTASNKTRLSQT<PG--IVYLYIKKVGKAPMSACGVCPGRLQGIYA

Parental  VRPKVLMRLSKTKKHVSRAYGGSMCAKCVRDRIKRAFL-IEEQKIVVKVLKAQAQSQKAK
          VRP.VL.RLSK..K.VS...G.SM.AKC..DR.K.AFL...EQ...VK.LKAQAQSQKAK
Retrocopy VRPQVLVRLSKILKSVSTTNGVSMTAKCIHDRTKHAFL<FKEQNVIVKMLKAQAQSQKAK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	67.14 RPM
SRP007412_cerebellum	0.04 RPM	96.60 RPM
SRP007412_heart	0.03 RPM	42.96 RPM
SRP007412_kidney	0.00 RPM	227.51 RPM
SRP007412_liver	0.00 RPM	244.87 RPM
SRP007412_testis	0.21 RPM	93.24 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1401 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1401 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1921
Pan troglodytes	retro_ptro_1285
Pongo abelii	retro_pabe_1609

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 140 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001758	20 retrocopies	retro_amel_1151, retro_amel_1298, retro_amel_1402, retro_amel_147, retro_amel_1595, retro_amel_1670, retro_amel_1678, retro_amel_1755, retro_amel_240, retro_amel_368, retro_amel_388, retro_amel_410, retro_amel_477, retro_amel_655, retro_amel_690, retro_amel_739, retro_amel_874, retro_amel_936, retro_amel_949, retro_amel_978,
Dasypus novemcinctus	ENSDNOG00000011179	26 retrocopies	retro_dnov_1172, retro_dnov_1775, retro_dnov_2020, retro_dnov_2025, retro_dnov_2079, retro_dnov_2127, retro_dnov_2137, retro_dnov_2275, retro_dnov_2385, retro_dnov_2501, retro_dnov_252, retro_dnov_262, retro_dnov_2627, retro_dnov_2651, retro_dnov_325, retro_dnov_339, retro_dnov_430, retro_dnov_553, retro_dnov_565, retro_dnov_59, retro_dnov_606, retro_dnov_635, retro_dnov_658, retro_dnov_862, retro_dnov_88, retro_dnov_978,
Gorilla gorilla	ENSGGOG00000007650	32 retrocopies	retro_ggor_1097, retro_ggor_1236, retro_ggor_1401 , retro_ggor_1471, retro_ggor_1604, retro_ggor_1657, retro_ggor_1878, retro_ggor_2123, retro_ggor_2249, retro_ggor_226, retro_ggor_2262, retro_ggor_2336, retro_ggor_2397, retro_ggor_2494, retro_ggor_2723, retro_ggor_2744, retro_ggor_2884, retro_ggor_3042, retro_ggor_308, retro_ggor_327, retro_ggor_462, retro_ggor_479, retro_ggor_561, retro_ggor_607, retro_ggor_638, retro_ggor_680, retro_ggor_696, retro_ggor_747, retro_ggor_760, retro_ggor_781, retro_ggor_975, retro_ggor_995,
Gadus morhua	ENSGMOG00000009982	1 retrocopy	retro_gmor_31,
Loxodonta africana	ENSLAFG00000032615	6 retrocopies	retro_lafr_1039, retro_lafr_1232, retro_lafr_182, retro_lafr_298, retro_lafr_306, retro_lafr_733,
Macropus eugenii	ENSMEUG00000009361	3 retrocopies	retro_meug_1012, retro_meug_1754, retro_meug_1775,
Macaca mulatta	ENSMMUG00000011901	1 retrocopy	retro_mmul_162,
Monodelphis domestica	ENSMODG00000020601	3 retrocopies	retro_mdom_1690, retro_mdom_774, retro_mdom_836,
Pongo abelii	ENSPPYG00000014988	18 retrocopies	retro_pabe_1171, retro_pabe_1351, retro_pabe_1609, retro_pabe_1630, retro_pabe_1859, retro_pabe_2338, retro_pabe_2560, retro_pabe_2784, retro_pabe_2931, retro_pabe_3330, retro_pabe_3352, retro_pabe_3375, retro_pabe_3788, retro_pabe_385, retro_pabe_420, retro_pabe_566, retro_pabe_77, retro_pabe_827,
Pelodiscus sinensis	ENSPSIG00000003295	1 retrocopy	retro_psin_60,
Sarcophilus harrisii	ENSSHAG00000001357	1 retrocopy	retro_shar_799,
Sarcophilus harrisii	ENSSHAG00000002052	3 retrocopies	retro_shar_131, retro_shar_324, retro_shar_419,
Tupaia belangeri	ENSTBEG00000003574	24 retrocopies	retro_tbel_1109, retro_tbel_1298, retro_tbel_1337, retro_tbel_1532, retro_tbel_1781, retro_tbel_1857, retro_tbel_1941, retro_tbel_213, retro_tbel_2162, retro_tbel_2165, retro_tbel_2372, retro_tbel_2391, retro_tbel_2601, retro_tbel_279, retro_tbel_335, retro_tbel_3606, retro_tbel_3984, retro_tbel_4059, retro_tbel_4398, retro_tbel_657, retro_tbel_74, retro_tbel_901, retro_tbel_974, retro_tbel_983,
Xenopus tropicalis	ENSXETG00000021095	1 retrocopy	retro_xtro_5,