RetrogeneDB ID: retro_ggor_1498

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 20:10632382..10633632(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSGGOG00000006441
• Aliases: None
• Description: None

Sequence

>retro_ggor_1498
GAGAAACAAAAAAACAAGAGAAAACCAGAGATGTTTAACTTTTCAGCCATTCACTTAATTCATGATCCCCAAGATTTTGC
AGAAAAACTACTAAAGCAGCTTGAGTGAAGTAAGAAGAAGTTTGAAGTGAAAATGATGCTCATGAACCTCATCTCCAGAT
TGGTGGGAATTCATGAGCTCTTTCTCTTCAATTTCTATCCTTGTTTGCAAAGGTTTCTGCAGCCCCACCAAAGAGAAGTA
ACAAAGATCCTCCGTTTGCTGCACAAGCATCTCATCACCTAGTACCCCCAGAGATTATTCAATCATTGCTTATGACTCTG
GCAAACAATTTGGTTACCAACAAGAACTCTGGAGAAGTCATGACAGTAGGAATCAATGCTATAAAAGAGATAACAGCTCG
ATGTTCTCTGGCCATGACTGAAGAACTTCTCCAAGACCTGGCTCAGTATAAAACACACAAGGATAAGAATGTAATGATGA
GTGCTAGAACTTTGATTCAGCTCTTCCGAACACTGAATCCTCAGATGCTGCAGAAGAAATTCCAGGGTAAGCCTACAGAG
TCCTCCATAGAAGCAAGAGTACAAGAATATGGAGAATTAGATGCTAAAGATTACATTCCAGGAGCAGAAGTTCTGGAAGG
TGAGAAAGAAGAGAATGCTGAAAATGATGAAGATGGATGGGAAAATACCAGTCTCAGTGAGGAGGAGGATGCTATTGGTG
AATGGATTGATGTGCAACACTCTTCTGATGAAGAACAGCAAGAAATCTCCAAGAAGCTGAACAGGATGCCCATGGAGGAG
CGGAAAGCCAAAGCTGCAGCCATCAGCACCAGCCAAGTTTTAACTCAGGAAGACTTCCAGAAAATCCGCATGGCCCAACT
GAGAAAAGAACTTGATGCTGCCCCTGGGAAATCCCAGAAGAGGAAATAAATTGAAATAGACAGTGATGAAGAGCCCAGGG
GTGAATTACTTTCTCTTCGGGACATCGAACGCCTTCATCAAAAGCCGAAGTCTGACAAAGAGACAAGACTAGCAACTGCA
ATGGCTAGAAAGACAGACGGAAAAGAATTTGTGAGGAAGAAAACCAAAATGAATCCATTTCCCAGTTTGACAAATAAAGA
GGAGAAAAAACAGAAGAATTTTATGATGATGCAGTATAGCCAGAATGTCCGGTGAAAAAATAAGCGTTCCTTCCGAGAAA
AACAGTTGGCGCTACGAGATGCACTTTTGAAAAAGAGAAAAAGAATGAAG

Alignment

ORF - retro_ggor_1498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 60.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKQKKKKKPEMFNFSAIHLIHDPQDFAEKLLKQLECCKERFEVKMMLMNLISRLVGIHELFLFNFYPFLQ
          .KQK.K.KPEMFNFSAIHLIHDPQDFAEKLLKQLE..K..FEVKMMLMNLISRLVGIHELFLFNFYP.LQ
Retrocopy EKQKNKRKPEMFNFSAIHLIHDPQDFAEKLLKQLE*SKKKFEVKMMLMNLISRLVGIHELFLFNFYPCLQ

Parental  RFLQPHQREVTKILL-FAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLAM
          RFLQPHQREVTKIL..FAAQASHHLVPPEIIQSLLMT.ANN.VT.KNSGEVMTVGINAIKEITARC.LAM
Retrocopy RFLQPHQREVTKILR<FAAQASHHLVPPEIIQSLLMTLANNLVTNKNSGEVMTVGINAIKEITARCSLAM

Parental  TEELLQDLAQYKTHKDKNVMMSARTLIHLFRTLNPQMLQKKFRGKPTEASIEARVQEYGELDAKDYIPGA
          TEELLQDLAQYKTHKDKNVMMSARTLI.LFRTLNPQMLQKKF.GKPTE.SIEARVQEYGELDAKDYIPGA
Retrocopy TEELLQDLAQYKTHKDKNVMMSARTLIQLFRTLNPQMLQKKFQGKPTESSIEARVQEYGELDAKDYIPGA

Parental  EVLEVEKEENAENDEDGWESTSLSEEEDADGEWIDVQHSSDEEQQEISKKLNSMPMEERKAKAAAISTSR
          EVLE.EKEENAENDEDGWE.TSLSEEEDA.GEWIDVQHSSDEEQQEISKKLN.MPMEERKAKAAAISTS.
Retrocopy EVLEGEKEENAENDEDGWENTSLSEEEDAIGEWIDVQHSSDEEQQEISKKLNRMPMEERKAKAAAISTSQ

Parental  VLTQEDFQKIRMAQMRKELDAAPGKSQKRKYIEIDSDEEPRGELLSLRDIERLHKKPKSDKETRLATAMA
          VLTQEDFQKIRMAQ.RKELDAAPGKSQKRK.IEIDSDEEPRGELLSLRDIERLH.KPKSDKETRLATAMA
Retrocopy VLTQEDFQKIRMAQLRKELDAAPGKSQKRK*IEIDSDEEPRGELLSLRDIERLHQKPKSDKETRLATAMA

Parental  GKTDRKEFVRKKTKTNPFSSSTNKEKKKQKNFMMMRYSQNVRSKNKRSFREKQLALRDALLKKRKRMK
          .KTD.KEFVRKKTK.NPF.S.TNKE.KKQKNFMMM.YSQNVR.KNKRSFREKQLALRDALLKKRKRMK
Retrocopy RKTDGKEFVRKKTKMNPFPSLTNKEEKKQKNFMMMQYSQNVR*KNKRSFREKQLALRDALLKKRKRMK

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	24.89 RPM
SRP007412_cerebellum	0.00 RPM	17.49 RPM
SRP007412_heart	0.00 RPM	3.53 RPM
SRP007412_kidney	0.04 RPM	19.26 RPM
SRP007412_liver	0.00 RPM	13.24 RPM
SRP007412_testis	0.00 RPM	45.17 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_1498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1498 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2412
Pan troglodytes	retro_ptro_1388
Pongo abelii	retro_pabe_1777
Macaca mulatta	retro_mmul_604

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008521	2 retrocopies	retro_cfam_1211, retro_cfam_515,
Cavia porcellus	ENSCPOG00000008524	2 retrocopies	retro_cpor_510, retro_cpor_994,
Echinops telfairi	ENSETEG00000004811	2 retrocopies	retro_etel_1946, retro_etel_779,
Homo sapiens	ENSG00000198301	2 retrocopies	retro_hsap_2412, retro_hsap_4030,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498 ,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Microcebus murinus	ENSMICG00000006682	1 retrocopy	retro_mmur_1204,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Oryctolagus cuniculus	ENSOCUG00000026953	1 retrocopy	retro_ocun_547,
Pongo abelii	ENSPPYG00000014852	1 retrocopy	retro_pabe_1777,
Pan troglodytes	ENSPTRG00000024399	2 retrocopies	retro_ptro_1388, retro_ptro_2732,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Sus scrofa	ENSSSCG00000008974	1 retrocopy	retro_sscr_571,
Tupaia belangeri	ENSTBEG00000005270	1 retrocopy	retro_tbel_2414,