RetrogeneDB ID: retro_ggor_1281

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 16:67298207..67298603(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAD2L1
• Ensembl ID: ENSGGOG00000002516
• Aliases: None
• Description: None

Sequence

>retro_ggor_1281
GCACTAAAGCTTTCCTGGGAGAAGGATATCACCTTGTGCAGGAGTGCCAAAATCGTGGTCAAGTTCTTCTCATTTGGCAT
CAACAGCATTTTATTTCAGCATGGCATATATCCATCTGGAACATTTACTCCAGTGTGGAAATATGTGCTCACCTTGCTTG
TAACCACTAATCTTGAGCTCATGAAACACCTAAATAACATGGTGGAACAACTAAAGCATAGGCTATACAAACGTTCAGGT
CAGAAACTGACTGGAGTCATCTCAACAATTGAAAGTGATGAGGTCCTTCAAAGATGGCAGTTTGACTCTAAGTGTGATAA
GACTGCAAAAGATCATCTTGGGCCCAGAGAATAGTTGCAGAAAACTATCCAGGATGAAATCTGTTTAGTAATCAGA

Alignment

ORF - retro_ggor_1281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.21 %
• Parental protein coverage: 64.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALQLSREQGITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQ
          AL.LS.E..ITL..SA.IV..FFSFGINSIL.Q.GIYPS.TFT.V.KY.LTLLVTT.LEL.K.LNN.VEQ
Retrocopy ALKLSWEKDITLCRSAKIVVKFFSFGINSILFQHGIYPSGTFTPVWKYVLTLLVTTNLELMKHLNNMVEQ

Parental  LKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVIR
          LK..LYK.S.QKL..VIS.IES.EVL.RWQFD..CDKTAKD...PRE..QK.IQDEI..VIR
Retrocopy LKHRLYKRSGQKLTGVISTIESDEVLQRWQFDSKCDKTAKDHLGPRE*LQKTIQDEICLVIR

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	1.77 RPM
SRP007412_cerebellum	0.00 RPM	0.75 RPM
SRP007412_heart	0.03 RPM	0.19 RPM
SRP007412_kidney	0.00 RPM	0.61 RPM
SRP007412_liver	0.03 RPM	0.47 RPM
SRP007412_testis	0.00 RPM	18.44 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_1281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1281 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1707
Pan troglodytes	retro_ptro_1156
Pongo abelii	retro_pabe_1403

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012813	2 retrocopies	retro_chof_1340, retro_chof_2524,
Dasypus novemcinctus	ENSDNOG00000013456	1 retrocopy	retro_dnov_1348,
Erinaceus europaeus	ENSEEUG00000009629	1 retrocopy	retro_eeur_446,
Echinops telfairi	ENSETEG00000015756	1 retrocopy	retro_etel_724,
Homo sapiens	ENSG00000164109	2 retrocopies	retro_hsap_1350, retro_hsap_1707,
Gorilla gorilla	ENSGGOG00000002516	1 retrocopy	retro_ggor_1281 ,
Loxodonta africana	ENSLAFG00000029619	1 retrocopy	retro_lafr_1138,
Myotis lucifugus	ENSMLUG00000011092	8 retrocopies	retro_mluc_1242, retro_mluc_165, retro_mluc_1802, retro_mluc_1904, retro_mluc_1986, retro_mluc_2434, retro_mluc_609, retro_mluc_696,
Macaca mulatta	ENSMMUG00000004875	2 retrocopies	retro_mmul_1292, retro_mmul_1701,
Monodelphis domestica	ENSMODG00000018944	1 retrocopy	retro_mdom_633,
Mus musculus	ENSMUSG00000029910	2 retrocopies	retro_mmus_1684, retro_mmus_2573,
Nomascus leucogenys	ENSNLEG00000009092	1 retrocopy	retro_nleu_1832,
Oryctolagus cuniculus	ENSOCUG00000008243	4 retrocopies	retro_ocun_1424, retro_ocun_1469, retro_ocun_1486, retro_ocun_752,
Otolemur garnettii	ENSOGAG00000004054	1 retrocopy	retro_ogar_199,
Pongo abelii	ENSPPYG00000015029	2 retrocopies	retro_pabe_1121, retro_pabe_1403,
Pan troglodytes	ENSPTRG00000016401	2 retrocopies	retro_ptro_1156, retro_ptro_925,
Ictidomys tridecemlineatus	ENSSTOG00000025410	2 retrocopies	retro_itri_1592, retro_itri_327,
Tupaia belangeri	ENSTBEG00000011065	3 retrocopies	retro_tbel_4460, retro_tbel_4666, retro_tbel_664,
Tursiops truncatus	ENSTTRG00000011017	1 retrocopy	retro_ttru_1754,