RetrogeneDB ID: retro_pabe_3434

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:92373249..92373766(+)
• Located in intron of: ENSPPYG00000019416

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSA2
• Ensembl ID: ENSPPYG00000025926
• Aliases: None
• Description: NSA2 ribosome biogenesis homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:30728]

Sequence

>retro_pabe_3434
ATGCCACAGAACGAATATATTGAATTACACCGTAAACACTATGGATACCGTTTGGATTACCAACAGAAAAAGAGAAAGAA
AGAAAGTGGAGAGGCTCATGAACGTTCAAAGGCGGCAAAGAAAATGATTGGTCTGAAGGCTAAGCTTTAACATAAACACC
GCCATGCTGAGAAAATACAAATGAAAAAGACTATCAAAGATTCATGAAAAGAGAAACACCAAACACAAGAATGATGAAAA
GACTCCACAGGGAGCAGTACCTGCCTATCTGCTGGACAGAGAGGGACAATCTCGAACTAAAGTACTTTCCAATATGATTA
AACAGAAACGAAAAGAAAAGGCAGGAAAATGGGAAGTCCCTCTGCCTAAAGTACGTGCCCAGGGAGAAGCAGAAGTATTA
AAAGTTATTCGAACAGGAAAGAGAAAGAAGGCATGGAAGAGGATGGTTACTAAAGTGTGCTTTGTTGGAGATGGCTTTAC
AAGAAAACCACCTAAATATGAAAGATTCATCAGGCCA

Alignment

ORF - retro_pabe_3434 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.86 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPQNEYIELHRKRYGYRLDYHEKKRKKESREAHERSKKANKMIGLKAKLYHKQRHAEKIQMKKTIK-MHE
          MPQNEYIELHRK.YGYRLDY..KKRKKES.EAHERSK.A.KMIGLKAKL.HK.RHAEKIQMKKTIK..HE
Retrocopy MPQNEYIELHRKHYGYRLDYQQKKRKKESGEAHERSKAAKKMIGLKAKL*HKHRHAEKIQMKKTIK>IHE

Parental  KRNTKQKNDEKTPQGAVPAYLLDREGQSRAKVLSNMIKQKRKEKAGKWEVPLPKVRAQGETEVLKKFIRT
          KRNTK.KNDEKTPQGAVPAYLLDREGQSR.KVLSNMIKQKRKEKAGKWEVPLPKVRAQGE.EVL.K.IRT
Retrocopy KRNTKHKNDEKTPQGAVPAYLLDREGQSRTKVLSNMIKQKRKEKAGKWEVPLPKVRAQGEAEVL-KVIRT

Parental  GKRKKKAWKRMVTKVCFVGDGFTRKPPKYERFIRP
          GKR.KKAWKRMVTKVCFVGDGFTRKPPKYERFIRP
Retrocopy GKR-KKAWKRMVTKVCFVGDGFTRKPPKYERFIRP

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	7.46 RPM	10.95 RPM
SRP007412_cerebellum	4.38 RPM	12.28 RPM
SRP007412_heart	4.40 RPM	14.60 RPM
SRP007412_kidney	12.53 RPM	23.40 RPM
SRP007412_liver	6.58 RPM	16.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3434 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3434 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3434 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 176 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008311	4 retrocopies	retro_cfam_1292, retro_cfam_361, retro_cfam_49, retro_cfam_64,
Callithrix jacchus	ENSCJAG00000016874	1 retrocopy	retro_cjac_116,
Cavia porcellus	ENSCPOG00000006648	1 retrocopy	retro_cpor_672,
Dasypus novemcinctus	ENSDNOG00000010615	1 retrocopy	retro_dnov_428,
Echinops telfairi	ENSETEG00000004095	13 retrocopies	retro_etel_1086, retro_etel_1479, retro_etel_1786, retro_etel_2030, retro_etel_2112, retro_etel_2116, retro_etel_2197, retro_etel_359, retro_etel_613, retro_etel_729, retro_etel_890, retro_etel_940, retro_etel_988,
Felis catus	ENSFCAG00000011978	1 retrocopy	retro_fcat_98,
Homo sapiens	ENSG00000164346	4 retrocopies	retro_hsap_1144, retro_hsap_1577, retro_hsap_4731, retro_hsap_493,
Gorilla gorilla	ENSGGOG00000014365	6 retrocopies	retro_ggor_1200, retro_ggor_2136, retro_ggor_2939, retro_ggor_463, retro_ggor_824, retro_ggor_891,
Loxodonta africana	ENSLAFG00000009910	4 retrocopies	retro_lafr_253, retro_lafr_455, retro_lafr_620, retro_lafr_714,
Macropus eugenii	ENSMEUG00000015798	3 retrocopies	retro_meug_1191, retro_meug_1408, retro_meug_161,
Microcebus murinus	ENSMICG00000000752	3 retrocopies	retro_mmur_1074, retro_mmur_374, retro_mmur_925,
Macaca mulatta	ENSMMUG00000011196	6 retrocopies	retro_mmul_1984, retro_mmul_2219, retro_mmul_2523, retro_mmul_408, retro_mmul_441, retro_mmul_890,
Monodelphis domestica	ENSMODG00000001900	4 retrocopies	retro_mdom_115, retro_mdom_1702, retro_mdom_581, retro_mdom_592,
Mustela putorius furo	ENSMPUG00000005795	5 retrocopies	retro_mputfur_153, retro_mputfur_250, retro_mputfur_510, retro_mputfur_573, retro_mputfur_690,
Nomascus leucogenys	ENSNLEG00000005046	10 retrocopies	retro_nleu_1026, retro_nleu_1507, retro_nleu_1758, retro_nleu_1759, retro_nleu_1929, retro_nleu_2255, retro_nleu_2565, retro_nleu_2675, retro_nleu_768, retro_nleu_943,
Oryctolagus cuniculus	ENSOCUG00000006536	6 retrocopies	retro_ocun_149, retro_ocun_1591, retro_ocun_1602, retro_ocun_306, retro_ocun_658, retro_ocun_76,
Ochotona princeps	ENSOPRG00000001867	7 retrocopies	retro_opri_1145, retro_opri_1195, retro_opri_254, retro_opri_427, retro_opri_654, retro_opri_778, retro_opri_83,
Pongo abelii	ENSPPYG00000025926	8 retrocopies	retro_pabe_1300, retro_pabe_1715, retro_pabe_240, retro_pabe_3434 , retro_pabe_3570, retro_pabe_3678, retro_pabe_950, retro_pabe_976,
Pan troglodytes	ENSPTRG00000016990	6 retrocopies	retro_ptro_1063, retro_ptro_1713, retro_ptro_2105, retro_ptro_3146, retro_ptro_372, retro_ptro_779,
Rattus norvegicus	ENSRNOG00000016530	15 retrocopies	retro_rnor_1074, retro_rnor_1317, retro_rnor_1366, retro_rnor_1921, retro_rnor_2630, retro_rnor_2745, retro_rnor_2767, retro_rnor_2817, retro_rnor_2820, retro_rnor_2852, retro_rnor_2877, retro_rnor_2964, retro_rnor_618, retro_rnor_945, retro_rnor_951,
Sorex araneus	ENSSARG00000009424	4 retrocopies	retro_sara_555, retro_sara_589, retro_sara_620, retro_sara_703,
Sarcophilus harrisii	ENSSHAG00000017654	5 retrocopies	retro_shar_292, retro_shar_336, retro_shar_495, retro_shar_679, retro_shar_745,
Ictidomys tridecemlineatus	ENSSTOG00000007959	3 retrocopies	retro_itri_1630, retro_itri_1638, retro_itri_860,
Tupaia belangeri	ENSTBEG00000012978	56 retrocopies	retro_tbel_1062, retro_tbel_1078, retro_tbel_1141, retro_tbel_1317, retro_tbel_1329, retro_tbel_1476, retro_tbel_152, retro_tbel_1548, retro_tbel_1569, retro_tbel_1627, retro_tbel_1733, retro_tbel_1762, retro_tbel_1778, retro_tbel_179, retro_tbel_1845, retro_tbel_1940, retro_tbel_2102, retro_tbel_2113, retro_tbel_2138, retro_tbel_2220, retro_tbel_229, retro_tbel_254, retro_tbel_2586, retro_tbel_2757, retro_tbel_2784, retro_tbel_3016, retro_tbel_3040, retro_tbel_3116, retro_tbel_3264, retro_tbel_3298, retro_tbel_3417, retro_tbel_3514, retro_tbel_3601, retro_tbel_3650, retro_tbel_3724, retro_tbel_3736, retro_tbel_3763, retro_tbel_3795, retro_tbel_4028, retro_tbel_406, retro_tbel_4104, retro_tbel_4169, retro_tbel_4270, retro_tbel_430, retro_tbel_4401, retro_tbel_4422, retro_tbel_4491, retro_tbel_4503, retro_tbel_4513, retro_tbel_4642, retro_tbel_4689, retro_tbel_535, retro_tbel_670, retro_tbel_721, retro_tbel_897, retro_tbel_91,