RetrogeneDB ID: retro_pabe_153

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:4306202..4307522(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000002941
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000025948
• Aliases: None
• Description: None

Sequence

>retro_pabe_153
ATGGGTCAAAGTCAGAGTGGTGGTGATGGTCCTGGAGGTGGCAAGAAGGATGACAAGGACAAGAAAAAGAAATATGAACC
TCCTGTACCAACTAGAGTGGGGAAAAAGAAGAAGAAAACAAAGGGACCAGATGCTGCCAGGAAACTGCCACTGGTGACAT
CTCACACTCAGTGCCGGTTAAAATTACTGAAGTTAGAGAGAATTAAAGACTATCTTCTCATGGAGGAAGAATTCATTAGA
AATCAGGAACAAATGAAGCCATTAGAAGAAAAGCAAGAGGAGGAAAGATCAAAAGTGGATGATCTGAGGGGGACCCCGAT
GTCAGTAGGAACCTTGGAAGAGATCATTGATGACAATCACGCCATCGTGTCTACATCTGTGGGCTCAGAACACTACATCA
GCATTCTTTCATTTGTAGACAAGGATCTGCTGGAACCTGGCTGCTTGGTCCTGCTCAACCACAAGGTGCATGCCGTGATA
GGGATGCTGATGGATGACACAGATCCCCTGGTCACAGTGATGAAGGTGGAAAAGGCCCCCCAGGAGACCTATGCGGATAT
TGGGGGGTTGGACAACCAAATTCAGGAAATTAAGGAATCTGTGGAGCTTCCTCTCACCCATCCTGAATATTATGAAGAGA
TGGGTATAAAGCCTCCTAAGGGGGTCATTCTCTGTGGTCCACCTGGCACGGGTAAAACCTTGTTAGCCAAAGCAGTAGCA
AACCAAACCTCAGCCACTTTCTTGAGAGTGGTTGGCTCTGAACTTATTCAGAAGTACCTAGGTGATGGGCCCAAACTCGT
ATGGGAATTGTTTCGAGTTGCTGAAGAACATGCACTGTCCATCATGTTTATTGATGAAATTGACGCCATTGGGACAAAAA
GATATGACTCCCATTCTGGTGGTGAGAGAGAAATTCAGCGAACAATGTTGGAACTGCTGTGCCAGTTGGATGGATTTGAT
TCTAGGGGAGATGTGAAAGTTATCACGGCCACAAACCGAACAGAAACTTTGGATCCAGCACTTATCAGACCAGGCCGCAT
TGACAGGAAGATTGAGCTCCCCCTGCCTGATGAAAAGACGAAGAAGCGCATCTTTCAGATTCACACAAGCAGGATGACGC
TGGCTGATGATGTAACCCTGGACGACTTGATCATGGCTAAAGATGACCTCTCTGGTGCTGACATCAAGGCAATCTGTACA
GAAGCTGGTCTGATGGCCTTAAGAGAATGTAGAATAAAAGTAACAAATGAAGACTTCAAAAAATCTAAAGAAAGTGTTCT
TTGTAAGAAACAGGAAGGCACCCCTGAGGGGCTGTATCTC

Alignment

ORF - retro_pabe_153 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.68 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRLKLLKLERIKD
          MGQSQSGG.GPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAA.KLPLVT.HTQCRLKLLKLERIKD
Retrocopy MGQSQSGGDGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAARKLPLVTSHTQCRLKLLKLERIKD

Parental  YLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNHAIVSTSVGSEHYVSILSFVD
          YLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNHAIVSTSVGSEHY.SILSFVD
Retrocopy YLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNHAIVSTSVGSEHYISILSFVD

Parental  KDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHPEY
          KDLLEPGC.VLLNHKVHAVIG.LMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHPEY
Retrocopy KDLLEPGCLVLLNHKVHAVIGMLMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHPEY

Parental  YEEMGIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPS
          YEEMGIKPPKGVIL.GPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLV.ELFRVAEEHA.S
Retrocopy YEEMGIKPPKGVILCGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVWELFRVAEEHALS

Parental  IVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRK
          I.FIDEIDAIGTKRYDS.SGGEREIQRTMLELL.QLDGFDSRGDVKVI.ATNR.ETLDPALIRPGRIDRK
Retrocopy IMFIDEIDAIGTKRYDSHSGGEREIQRTMLELLCQLDGFDSRGDVKVITATNRTETLDPALIRPGRIDRK

Parental  IEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
          IE.PLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRE.R.KVTNEDFK
Retrocopy IELPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRECRIKVTNEDFK

Parental  KSKENVLYKKQEGTPEGLYL
          KSKE.VL.KKQEGTPEGLYL
Retrocopy KSKESVLCKKQEGTPEGLYL

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	0.17 RPM	52.80 RPM
SRP007412_cerebellum	0.00 RPM	42.93 RPM
SRP007412_heart	0.06 RPM	32.33 RPM
SRP007412_kidney	0.10 RPM	37.82 RPM
SRP007412_liver	0.12 RPM	34.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_153 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_153 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 101 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001839	4 retrocopies	retro_amel_1536, retro_amel_1886, retro_amel_405, retro_amel_962,
Canis familiaris	ENSCAFG00000017510	2 retrocopies	retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni	ENSCHOG00000013595	1 retrocopy	retro_chof_1954,
Callithrix jacchus	ENSCJAG00000017701	7 retrocopies	retro_cjac_1152, retro_cjac_1537, retro_cjac_2417, retro_cjac_2433, retro_cjac_4219, retro_cjac_661, retro_cjac_678,
Cavia porcellus	ENSCPOG00000002424	1 retrocopy	retro_cpor_144,
Dasypus novemcinctus	ENSDNOG00000006458	1 retrocopy	retro_dnov_2162,
Equus caballus	ENSECAG00000003601	1 retrocopy	retro_ecab_355,
Echinops telfairi	ENSETEG00000002661	1 retrocopy	retro_etel_580,
Felis catus	ENSFCAG00000011310	8 retrocopies	retro_fcat_1444, retro_fcat_1559, retro_fcat_2015, retro_fcat_344, retro_fcat_614, retro_fcat_691, retro_fcat_713, retro_fcat_924,
Homo sapiens	ENSG00000100764	10 retrocopies	retro_hsap_1090, retro_hsap_1278, retro_hsap_2080, retro_hsap_2658, retro_hsap_2810, retro_hsap_2873, retro_hsap_3323, retro_hsap_3416, retro_hsap_3793, retro_hsap_975,
Gorilla gorilla	ENSGGOG00000010620	8 retrocopies	retro_ggor_1004, retro_ggor_1298, retro_ggor_1629, retro_ggor_1954, retro_ggor_1993, retro_ggor_2309, retro_ggor_780, retro_ggor_858,
Macropus eugenii	ENSMEUG00000001526	1 retrocopy	retro_meug_623,
Microcebus murinus	ENSMICG00000016733	7 retrocopies	retro_mmur_1039, retro_mmur_1063, retro_mmur_1245, retro_mmur_1577, retro_mmur_216, retro_mmur_839, retro_mmur_983,
Myotis lucifugus	ENSMLUG00000007471	2 retrocopies	retro_mluc_2490, retro_mluc_508,
Macaca mulatta	ENSMMUG00000022990	1 retrocopy	retro_mmul_255,
Mustela putorius furo	ENSMPUG00000008150	4 retrocopies	retro_mputfur_1602, retro_mputfur_409, retro_mputfur_654, retro_mputfur_815,
Mus musculus	ENSMUSG00000021178	3 retrocopies	retro_mmus_1517, retro_mmus_1826, retro_mmus_812,
Nomascus leucogenys	ENSNLEG00000017013	10 retrocopies	retro_nleu_1123, retro_nleu_1163, retro_nleu_1589, retro_nleu_1625, retro_nleu_1669, retro_nleu_2318, retro_nleu_2625, retro_nleu_429, retro_nleu_616, retro_nleu_706,
Oryctolagus cuniculus	ENSOCUG00000006231	4 retrocopies	retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii	ENSOGAG00000032343	2 retrocopies	retro_ogar_3014, retro_ogar_367,
Pongo abelii	ENSPPYG00000025948	9 retrocopies	retro_pabe_1059, retro_pabe_153 , retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Pan troglodytes	ENSPTRG00000006623	9 retrocopies	retro_ptro_1530, retro_ptro_1904, retro_ptro_1944, retro_ptro_2153, retro_ptro_2321, retro_ptro_2573, retro_ptro_672, retro_ptro_742, retro_ptro_874,
Pteropus vampyrus	ENSPVAG00000010020	3 retrocopies	retro_pvam_1190, retro_pvam_350, retro_pvam_500,
Ictidomys tridecemlineatus	ENSSTOG00000001655	1 retrocopy	retro_itri_780,
Tursiops truncatus	ENSTTRG00000013582	1 retrocopy	retro_ttru_239,