RetrogeneDB ID: retro_pabe_3410

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:51239009..51239690(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL7L1
• Ensembl ID: ENSPPYG00000016619
• Aliases: None
• Description: 60S ribosomal protein L7-like 1 [Source:RefSeq peptide;Acc:NP_001124607]

Sequence

>retro_pabe_3410
AAAAAGAGTTTTTATCAAGCTCTGAAAGCCACTCACTAAAGCCAGCACTTTTGTCAAGGAAGGAGCAGAGGAAAGGAAAA
GACCAGGGCTTAAGTGACTGGAATCATTTCTGCATGATTCTTGGTGGCAGAAATGAGACATAGTGCATCCCAGACAACAC
TAAGTGAAACCTCATGTCTTGGAATTGCCAAATAAACATTACTTGGCCATCGTTGTATGCATCCATAGGATTAATGGTGT
GAGTTTACTGTTGCAGATAATCATTCCAAGACTTCGCCTGAATAAGAAAATTTTCAATGATGTCTTTGTAAAAGTCACCC
CTGAGAGTCTAAAAAATGCTTTGAATACTAGAACCTTATGTGACCTGTGGATTTCCAAATCTGAAGCCTGTCCAGGAACC
CATCTTGAAAGACGGACAAGCCACGGTCAATAATAAACCACCTCTCTAACAGACAACAGAGTAATTGAGGAGCACCTGGG
GAGGTTTGGTGTGATTTGTTTGGAAGACCTCATTCATGAAAGTGCCTTCCTGGAGAAGTATTTCCAGAGATCTCATGATT
CTCAGGGCCTCACCTCTCCATGGCTTATCATAGCTACCAAGAATAGAGTGGGCTTCCTCAAGACATGGGCTCACCTGACT
ATTAGGGTGAATGCATTAATCAGCTCATCCACTAACTGAAC

Alignment

ORF - retro_pabe_3410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.22 %
• Parental protein coverage: 90.48 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  KRKAYQALKATQ-AKQALLAKKEQRKGKGLRF-KRLESFLHDSWRQKRDMVRLRRLEMKPHALELPDKHS
          K...YQALKAT...K.ALL..KEQRKGK.....K.LESFLHDSW.QK.D.V..R....KPH.LELP.KH.
Retrocopy KKSFYQALKATH<LKPALLSRKEQRKGKDQGL<K*LESFLHDSWWQK*DIVHPRQH*VKPHVLELPNKHY

Parental  LAFVVRIERIDGVSLLVQRTIARLRL-KKIFSGVFVKVTPQNL-KMLRIVEPYVTWGFPNLKSVRELILK
          LA.VV.I.RI.GVSLL.Q..I.RLRL.KKIF..VFVKVTP..L.KML.I.EPYVT.GFPNLK.V.E.ILK
Retrocopy LAIVVCIHRINGVSLLLQIIIPRLRLNKKIFNDVFVKVTPESL>KML*ILEPYVTCGFPNLKPVQEPILK

Parental  RGQAKVKNK-TIPLTDNTVIEEHLGKFGVICLEDLIHEIAF-PGKHFQEISWFLRPFHLSVARH-ATKNR
          .GQA.V.NK.T..LTDN.VIEEHLG.FGVICLEDLIHE.AF.PG..F.EIS.F..P.HLS.A.H.ATKNR
Retrocopy DGQATVNNK<TTSLTDNRVIEEHLGRFGVICLEDLIHESAF<PGEVFPEIS*FSGP-HLSMAYH>ATKNR

Parental  VGFLK-EMGTPGYRGERINQLIRQLN
          VGFLK..MG.P.Y.GE.INQLI..LN
Retrocopy VGFLK<DMGSPDY*GECINQLIH*LN

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	86.53 RPM
SRP007412_cerebellum	0.00 RPM	71.74 RPM
SRP007412_heart	0.00 RPM	35.79 RPM
SRP007412_kidney	0.00 RPM	77.63 RPM
SRP007412_liver	0.00 RPM	51.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3410 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3410 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3410 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 137 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012791	2 retrocopies	retro_amel_1260, retro_amel_243,
Bos taurus	ENSBTAG00000018478	2 retrocopies	retro_btau_588, retro_btau_816,
Canis familiaris	ENSCAFG00000001728	4 retrocopies	retro_cfam_1180, retro_cfam_1464, retro_cfam_1638, retro_cfam_330,
Choloepus hoffmanni	ENSCHOG00000000306	4 retrocopies	retro_chof_1168, retro_chof_1404, retro_chof_388, retro_chof_478,
Cavia porcellus	ENSCPOG00000021189	2 retrocopies	retro_cpor_1134, retro_cpor_653,
Dasypus novemcinctus	ENSDNOG00000013485	1 retrocopy	retro_dnov_689,
Equus caballus	ENSECAG00000003113	1 retrocopy	retro_ecab_998,
Erinaceus europaeus	ENSEEUG00000010431	1 retrocopy	retro_eeur_90,
Echinops telfairi	ENSETEG00000002419	3 retrocopies	retro_etel_1151, retro_etel_1823, retro_etel_542,
Felis catus	ENSFCAG00000009707	1 retrocopy	retro_fcat_143,
Gorilla gorilla	ENSGGOG00000009958	15 retrocopies	retro_ggor_1009, retro_ggor_1013, retro_ggor_1253, retro_ggor_1261, retro_ggor_1904, retro_ggor_2099, retro_ggor_2108, retro_ggor_2113, retro_ggor_2162, retro_ggor_2282, retro_ggor_2457, retro_ggor_2524, retro_ggor_2591, retro_ggor_2659, retro_ggor_2973,
Macaca mulatta	ENSMMUG00000021313	1 retrocopy	retro_mmul_11,
Monodelphis domestica	ENSMODG00000019028	1 retrocopy	retro_mdom_1708,
Mustela putorius furo	ENSMPUG00000013296	1 retrocopy	retro_mputfur_1577,
Mus musculus	ENSMUSG00000063888	4 retrocopies	retro_mmus_2359, retro_mmus_3172, retro_mmus_3626, retro_mmus_777,
Otolemur garnettii	ENSOGAG00000012671	3 retrocopies	retro_ogar_1380, retro_ogar_3358, retro_ogar_3428,
Pongo abelii	ENSPPYG00000016619	21 retrocopies	retro_pabe_1064, retro_pabe_1069, retro_pabe_1315, retro_pabe_1341, retro_pabe_1370, retro_pabe_1379, retro_pabe_1457, retro_pabe_2078, retro_pabe_2154, retro_pabe_2354, retro_pabe_2527, retro_pabe_2543, retro_pabe_2598, retro_pabe_2609, retro_pabe_2644, retro_pabe_2988, retro_pabe_3053, retro_pabe_3259, retro_pabe_3410 , retro_pabe_3714, retro_pabe_3753,
Pongo abelii	ENSPPYG00000018671	50 retrocopies	retro_pabe_1025, retro_pabe_1061, retro_pabe_1087, retro_pabe_1326, retro_pabe_1454, retro_pabe_1520, retro_pabe_1642, retro_pabe_1677, retro_pabe_1908, retro_pabe_1998, retro_pabe_2004, retro_pabe_2118, retro_pabe_2197, retro_pabe_2348, retro_pabe_2656, retro_pabe_2690, retro_pabe_2762, retro_pabe_2796, retro_pabe_2807, retro_pabe_2808, retro_pabe_2856, retro_pabe_2886, retro_pabe_2936, retro_pabe_2946, retro_pabe_307, retro_pabe_3085, retro_pabe_3117, retro_pabe_3139, retro_pabe_3191, retro_pabe_3414, retro_pabe_3468, retro_pabe_3506, retro_pabe_352, retro_pabe_3622, retro_pabe_3651, retro_pabe_3662, retro_pabe_3669, retro_pabe_3675, retro_pabe_436, retro_pabe_497, retro_pabe_514, retro_pabe_551, retro_pabe_628, retro_pabe_655, retro_pabe_826, retro_pabe_844, retro_pabe_859, retro_pabe_865, retro_pabe_867, retro_pabe_933,
Pteropus vampyrus	ENSPVAG00000008696	3 retrocopies	retro_pvam_1179, retro_pvam_1482, retro_pvam_975,
Rattus norvegicus	ENSRNOG00000016269	1 retrocopy	retro_rnor_2795,
Sorex araneus	ENSSARG00000005286	2 retrocopies	retro_sara_100, retro_sara_211,
Sarcophilus harrisii	ENSSHAG00000011219	1 retrocopy	retro_shar_216,
Sus scrofa	ENSSSCG00000026472	3 retrocopies	retro_sscr_198, retro_sscr_756, retro_sscr_807,
Ictidomys tridecemlineatus	ENSSTOG00000009841	2 retrocopies	retro_itri_1233, retro_itri_417,
Tursiops truncatus	ENSTTRG00000006971	6 retrocopies	retro_ttru_1194, retro_ttru_171, retro_ttru_361, retro_ttru_498, retro_ttru_528, retro_ttru_915,
Vicugna pacos	ENSVPAG00000008894	2 retrocopies	retro_vpac_386, retro_vpac_584,