RetrogeneDB ID: retro_pabe_1271

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:98792095..98792407(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000017272
• Aliases: None
• Description: None

Sequence

>retro_pabe_1271
GCTGCATTTCAACACGGAAAGACACCTCCTGCTCCATTCTCCACTCCTCCTGCAGGGGCAGGGATCCCACTTCCCTCAGT
GTCTGGGTCCTCCTCGCCACCCTGGTGTGATGCTAGCACCCTCTATGGGGGGTCCTCCTATGATGCCAATGACAGGCCCA
CCTCCTCCTGAGGGTGATGCCAGGGGATCTGCTCCTGGAATGAGGCCACCCATGGGATGTCACATGCCAGTGCTACCCGG
GCCCCCAGGATGAGCCCTCCCACCCATCGCATGGTGGAGCCCACGCAGCCCAGAATAACTAAGCCAGACAGA

Alignment

ORF - retro_pabe_1271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAFQQGKIPPTPFSAPPPAGAMIPPPPSLPG-PPR-PGMMPAPHMGGPPMMPMMGPPPPGMMPVGPAPGM
          AAFQ.GK.PP.PFS.PP.AGA.I.P.PS..G.PPR.PG.M.AP.MGGPPMMPM.GPPPP.....G.APGM
Retrocopy AAFQHGKTPPAPFSTPP-AGAGI-PLPSVSG>PPRHPGVMLAPSMGGPPMMPMTGPPPPEGDARGSAPGM

Parental  RPPMGGHMPMMPGP-PMMRPPARPMMVPTRPGMTRPDR
          RPPMG.HMP..PGP.P.M.PP...M..PT.P..T.PDR
Retrocopy RPPMGCHMPVLPGP<PRMSPPTHRMVEPTQPRITKPDR

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	12.88 RPM
SRP007412_cerebellum	0.00 RPM	9.73 RPM
SRP007412_heart	0.00 RPM	8.46 RPM
SRP007412_kidney	0.00 RPM	17.04 RPM
SRP007412_liver	0.00 RPM	13.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1271 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1271 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1531
Pan troglodytes	retro_ptro_1037
Callithrix jacchus	retro_cjac_2785

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 121 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000963	7 retrocopies	retro_amel_1237, retro_amel_1249, retro_amel_149, retro_amel_1522, retro_amel_1523, retro_amel_592, retro_amel_988,
Bos taurus	ENSBTAG00000024549	1 retrocopy	retro_btau_1636,
Canis familiaris	ENSCAFG00000001231	3 retrocopies	retro_cfam_348, retro_cfam_402, retro_cfam_409,
Felis catus	ENSFCAG00000005876	12 retrocopies	retro_fcat_1008, retro_fcat_1088, retro_fcat_1265, retro_fcat_1545, retro_fcat_1599, retro_fcat_161, retro_fcat_1664, retro_fcat_1814, retro_fcat_446, retro_fcat_578, retro_fcat_627, retro_fcat_922,
Homo sapiens	ENSG00000124562	6 retrocopies	retro_hsap_1531, retro_hsap_1866, retro_hsap_2865, retro_hsap_3195, retro_hsap_3829, retro_hsap_4241,
Loxodonta africana	ENSLAFG00000013534	2 retrocopies	retro_lafr_621, retro_lafr_878,
Myotis lucifugus	ENSMLUG00000002488	8 retrocopies	retro_mluc_1246, retro_mluc_1627, retro_mluc_2020, retro_mluc_2099, retro_mluc_2144, retro_mluc_2332, retro_mluc_735, retro_mluc_962,
Monodelphis domestica	ENSMODG00000013904	1 retrocopy	retro_mdom_22,
Mustela putorius furo	ENSMPUG00000003210	7 retrocopies	retro_mputfur_1233, retro_mputfur_1260, retro_mputfur_1396, retro_mputfur_374, retro_mputfur_441, retro_mputfur_519, retro_mputfur_531,
Mus musculus	ENSMUSG00000024217	21 retrocopies	retro_mmus_1079, retro_mmus_1084, retro_mmus_1231, retro_mmus_1313, retro_mmus_1374, retro_mmus_1400, retro_mmus_1515, retro_mmus_1649, retro_mmus_1673, retro_mmus_1781, retro_mmus_1876, retro_mmus_2087, retro_mmus_2211, retro_mmus_2506, retro_mmus_2973, retro_mmus_3089, retro_mmus_3366, retro_mmus_431, retro_mmus_531, retro_mmus_566, retro_mmus_638,
Oryctolagus cuniculus	ENSOCUG00000026668	3 retrocopies	retro_ocun_1019, retro_ocun_184, retro_ocun_196,
Otolemur garnettii	ENSOGAG00000008755	9 retrocopies	retro_ogar_1040, retro_ogar_130, retro_ogar_1763, retro_ogar_183, retro_ogar_2434, retro_ogar_3064, retro_ogar_3322, retro_ogar_3377, retro_ogar_697,
Procavia capensis	ENSPCAG00000016885	1 retrocopy	retro_pcap_34,
Pongo abelii	ENSPPYG00000017272	4 retrocopies	retro_pabe_1271 , retro_pabe_3066, retro_pabe_3225, retro_pabe_915,
Pongo abelii	ENSPPYG00000029902	3 retrocopies	retro_pabe_2367, retro_pabe_3397, retro_pabe_3524,
Pteropus vampyrus	ENSPVAG00000015597	1 retrocopy	retro_pvam_1213,
Rattus norvegicus	ENSRNOG00000000493	30 retrocopies	retro_rnor_1027, retro_rnor_1079, retro_rnor_1100, retro_rnor_1196, retro_rnor_1219, retro_rnor_1421, retro_rnor_1628, retro_rnor_1637, retro_rnor_1701, retro_rnor_1761, retro_rnor_2259, retro_rnor_2261, retro_rnor_2385, retro_rnor_2480, retro_rnor_2663, retro_rnor_2875, retro_rnor_2893, retro_rnor_445, retro_rnor_483, retro_rnor_495, retro_rnor_502, retro_rnor_630, retro_rnor_705, retro_rnor_706, retro_rnor_707, retro_rnor_730, retro_rnor_747, retro_rnor_778, retro_rnor_802, retro_rnor_889,
Sarcophilus harrisii	ENSSHAG00000000945	1 retrocopy	retro_shar_112,
Sus scrofa	ENSSSCG00000001531	1 retrocopy	retro_sscr_709,