RetrogeneDB ID: retro_pabe_2111

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:43253092..43254287(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA1
• Ensembl ID: ENSPPYG00000019141
• Aliases: None
• Description: DnaJ homolog subfamily A member 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5NVI9]

Sequence

>retro_pabe_2111
ATGGTGAAATAAACCACTTTCCATGATTTTTAGAGGGTCAAACAAAGTACCACTAAGGAAGAATTTAAAAAGGCTTATAG
GAAACTGGCCTTGAAGTACCACCCTGATAAAAATCCAAATGGAGAGAAGTTTAAACGAATTTCTCAAACTTACAAAGTTA
TTTCTGATGCCAAGAAAAGGGAATTATACAACAAAGGAAGATAACAGGTAAATAAGAGCGCTGAGCAAGTGGCAGTTCTG
GGTCCCCTATGGACATCTTCAACATAATTATTTATGGAGGAAGAAGAATGCAGAGAGAAAAGAGGAGTAACATTGTTGTG
CATCAGCTCTCAAAAACCTTAGAAAATGTATGTGATGGTACAACAAGAAAATTGGCACTTCACAAGAATGTAATTTGTGA
CTAATGTGAAGGCAGAAGTGGGGAAAAAAAGAGGAGAGAAGGATAGTGTTGTCCCAATTGCCAAGTTACTGGACTGCAAA
TAAGAATTCATGCAATAGGGCCTGGGATGGTTCAGCACACTTAGTCTGTGTGCATGCATGGAGTGCCACGGTCATGGAGA
ATGAATCAGTCCTAAAGATAGATGTAAACACGAAAATGGAAGAAAGATAGTTTGAGGGAAAAAGATTCTAGAAGTTCATG
TTGACAATGACATGAAATATGGCCAGAAGATAACATTTCATGGTGAAGGAGACAAAGAACCCGGATTGGAGCCAGGAGAT
ATTATCATTGAGTTAGATGAAAAGGACCATGCTGTTTTTACTTGACAAGAAGACTAGTTTATGTCTATGGACAGACAGCT
GGTTAAAATATTGTGTGGTTTCCAAAAACCAATATCCACTCTTGATTACTGAACTATAGTCATCACCTCTCACCCAGGTC
AGACTGTCAAATATGGAGAAATCAAATGTGTGCTAAATGAAGTCATGCCAATTTTTCATAGACCATATGAAAAGCATCAC
CTAATCATCAAATTCAAGGTAAACTTTCCTGAGAATGGTTTTCTCTCTCATGATAAGCTCTCTTAGTTGGGTAAACTCCT
ACCTGACAGGAAGGAAATAGAAGAGATTGTTGAAATGGATCAAGTTAAAACTGGTGTACTTTGATTCAGATCAGGAAAAA
CAGCACTATTGCAATGGAGAAACATGTGAGGATGATAAACATCATCCCAGAGGCGGTGTTCACTGCCAAACTTCA

Alignment

ORF - retro_pabe_2111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.22 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 13
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKGGEQ
          MVK.TT..D...VK...T.EE.KKAYRKLALKYHPDKNPN.GEKFK.ISQ.Y.V.SDAKKRELY.KG..Q
Retrocopy MVK*TTFHDF*RVKQSTTKEEFKKAYRKLALKYHPDKNPN-GEKFKRISQTYKVISDAKKRELYNKGR*Q

Parental  AIK-EGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEG
          ..K.E..A.G..GSPMDIF.....GG.RMQRE.R...VVHQLS.TLE....G.TRKLAL.KNVICD.CEG
Retrocopy VNK<ER*ASGSSGSPMDIFNIIIYGGRRMQREKRSNIVVHQLSKTLENVCDGTTRKLALHKNVICD*CEG

Parental  RGGKKGAVE--CCPNCRGTGMQIRIH-QIGPGMVQQIQ-SVCMECQGHGERISPKDRCKSCNGRKIVREK
          R.G.K...E..CCPNC..TG.QIRIH.Q.G.G.........CMEC.GHGE.ISPKDRCK..NGRKIV..K
Retrocopy RSGEKKRREG*CCPNCQVTGLQIRIH>Q*GLGWFSTLSLCACMECHGHGE*ISPKDRCKHENGRKIV*GK

Parental  KILEVHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQK
          KILEVH.D..MK.GQKITFHGEGD.EPGLEPGDIII.LD.KDHAVFT...ED.FM.MD.QLV..LCGFQK
Retrocopy KILEVHVDNDMKYGQKITFHGEGDKEPGLEPGDIIIELDEKDHAVFT*Q-ED*FMSMDRQLVKILCGFQK

Parental  PISTLDNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKL
          PISTLD..TIVITSHPGQ.VK.G.IKCVLNE.MPI..RPYEK..LII.FKVNFPENGFLS.DKLS.L.KL
Retrocopy PISTLDY*TIVITSHPGQTVKYGEIKCVLNEVMPIFHRPYEKHHLIIKFKVNFPENGFLSHDKLS*LGKL

Parental  LPERKEVEETDEMDQV-ELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS
          LP.RKE.EE..EMDQV..LV.FD..QE.....NGE..EDD.HHPRGGV.CQTS
Retrocopy LPDRKEIEEIVEMDQV>KLVYFDSDQEKQHYCNGETCEDDKHHPRGGVHCQTS

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	296.47 RPM
SRP007412_cerebellum	0.00 RPM	195.90 RPM
SRP007412_heart	0.00 RPM	92.21 RPM
SRP007412_kidney	0.00 RPM	197.16 RPM
SRP007412_liver	0.00 RPM	280.16 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2111 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2111 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2331
Pan troglodytes	retro_ptro_1705
Callithrix jacchus	retro_cjac_2730

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 128 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Bos taurus	ENSBTAG00000016265	6 retrocopies	retro_btau_1440, retro_btau_1599, retro_btau_1800, retro_btau_1826, retro_btau_574, retro_btau_828,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Callithrix jacchus	ENSCJAG00000008022	10 retrocopies	retro_cjac_1645, retro_cjac_1777, retro_cjac_2015, retro_cjac_2120, retro_cjac_2730, retro_cjac_2731, retro_cjac_2763, retro_cjac_3037, retro_cjac_3762, retro_cjac_887,
Cavia porcellus	ENSCPOG00000000462	6 retrocopies	retro_cpor_1456, retro_cpor_225, retro_cpor_386, retro_cpor_396, retro_cpor_561, retro_cpor_781,
Dasypus novemcinctus	ENSDNOG00000018342	3 retrocopies	retro_dnov_1139, retro_dnov_640, retro_dnov_884,
Felis catus	ENSFCAG00000008729	5 retrocopies	retro_fcat_1241, retro_fcat_1407, retro_fcat_1502, retro_fcat_1984, retro_fcat_811,
Homo sapiens	ENSG00000086061	4 retrocopies	retro_hsap_2331, retro_hsap_2569, retro_hsap_3647, retro_hsap_4889,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Myotis lucifugus	ENSMLUG00000016086	7 retrocopies	retro_mluc_1245, retro_mluc_1485, retro_mluc_1737, retro_mluc_1878, retro_mluc_2062, retro_mluc_2579, retro_mluc_576,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Mustela putorius furo	ENSMPUG00000004231	2 retrocopies	retro_mputfur_1543, retro_mputfur_487,
Nomascus leucogenys	ENSNLEG00000005268	4 retrocopies	retro_nleu_1255, retro_nleu_2550, retro_nleu_2793, retro_nleu_509,
Oryctolagus cuniculus	ENSOCUG00000004833	2 retrocopies	retro_ocun_516, retro_ocun_70,
Pongo abelii	ENSPPYG00000019141	4 retrocopies	retro_pabe_1892, retro_pabe_2111 , retro_pabe_2559, retro_pabe_2994,
Pan troglodytes	ENSPTRG00000020852	4 retrocopies	retro_ptro_1499, retro_ptro_1705, retro_ptro_177, retro_ptro_2472,
Rattus norvegicus	ENSRNOG00000007029	2 retrocopies	retro_rnor_2208, retro_rnor_608,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Ictidomys tridecemlineatus	ENSSTOG00000005200	4 retrocopies	retro_itri_265, retro_itri_303, retro_itri_378, retro_itri_809,
Tupaia belangeri	ENSTBEG00000000596	23 retrocopies	retro_tbel_1281, retro_tbel_134, retro_tbel_1529, retro_tbel_1542, retro_tbel_2260, retro_tbel_2293, retro_tbel_2316, retro_tbel_2428, retro_tbel_2445, retro_tbel_2917, retro_tbel_2965, retro_tbel_2972, retro_tbel_329, retro_tbel_3345, retro_tbel_3353, retro_tbel_3692, retro_tbel_4014, retro_tbel_4223, retro_tbel_432, retro_tbel_591, retro_tbel_617, retro_tbel_634, retro_tbel_842,
Tursiops truncatus	ENSTTRG00000007387	4 retrocopies	retro_ttru_1181, retro_ttru_1551, retro_ttru_567, retro_ttru_783,