RetrogeneDB ID: retro_pabe_2972

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:81319932..81321127(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSPPYG00000004654
• Aliases: None
• Description: citrate synthase [Source:HGNC Symbol;Acc:2422]

Sequence

>retro_pabe_2972
ATGGCTTTACTCACTACTGTCACCCAGTTCTTGGGAACGAAGGACGTATCTTGTCTCGTTCTTGCTGCCTGGCATGCCAG
TACCTCTTCCAGGAATTTGGAAGACATATCAGCTTACCTCATTCCCAAGGAGCAGGCCAGAATTAAGATCTTCCGACAGC
AACGTGGCAAGAGGGTAGTGGGCCAAAACACTGTGGGCATGATGTGTGGTGACCTGAGAGGCAAGAAGGGACTGGTATAT
GAAACATCAGTTCTTGATCCTAATGAAAGCATCCATTTCTGAGGCTTTAGTGTCCCTGGGTGCCAAAAACCGCCACCTAA
GGCTAAAGGTAAGAAAGAACCACTGCTGGAGGGTTTATTTCAGCTGCTGGTGGCTGAACAGATCCCAACAGAGGACAAAG
GCATCTTGGCTTTCAAAAAAGTGGGCAAAAAGGACAGCTCTACCCTCCCTTGTGGTCATCATGCTGGACAACTTTCCCAC
CAATATACTTCCCATGTCTCAGCTCAGTGCAGCTTTTACAGCCCTCAACAGTGAAAGTAATACTGCCTGAGCATATGCAG
AGGGTATCAAGTACCGGGAGCTGATTTATGAAGACTGTGTGGATCTGATCACAACGCTACCTGTGTTGCAGCAAAGATCT
ACCAATATCTCTACTAAAAGGGCAAAAATGTTGGGGGCATTGACTCCAAGCTGCACTGGCCCCACAATTTCACCAACATG
TTAGGCTATACTGATGCTCAGCTCACTGAGCTCATGCATCTGTACCACACCATCCACAGTGACCATAAGAGCAGCAATGT
AAGTGCCTATATCAGCAACTTGTTGGGCAGTGCCCCTTCGAGCCCTTATCTGTCCTTTGCAACAGCCATGAATGGATTGA
CAGGCCCTCTATGTGTACTAACAAATCAGGTGGTGCTTGTCTGGCTAACTTAACTACAGAAGGAAGTTGGCAAAGATGTG
GCAGAAGAGAAGTTATGAGACTACACCTGGAACACACTCAACCCAAGATGAAGTTATTCCAGACTATGGCCATGTAGTGC
TAAAGAAGATTGATCCACGAGGTACTTGCTGTGAGAGTTTGCTCTGAAACACCACATAATGACCGCATGTTAACTTGGTT
GCTCAACTACACAAGATTGTGCCCAATATCCTCTTAGAGAATGGCAAGGCCAAGAATCCTTGGTCCAATGTAGAT

Alignment

ORF - retro_pabe_2972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.34 %
• Parental protein coverage: 86.24 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MALLTAAARLLGTKNASCLVLAARHASASSTNLKDILADLIPKEQAKIKTFRQQHGKTVVGQITVDMMYG
          MALLT.....LGTK..SCLVLAA.HAS.SS.NL.DI.A.LIPKEQA.IK.FRQQ.GK.VVGQ.TV.MM.G
Retrocopy MALLTTVTQFLGTKDVSCLVLAAWHASTSSRNLEDISAYLIPKEQARIKIFRQQRGKRVVGQNTVGMMCG

Parental  GMRGMKGLVYETSVLDPDEGIRFRGFSIPECQKLLPKAKGGEEPLPEGLFWLLVTGHIPTEE-QVSWLSK
          ..RG.KGLVYETSVLDP.E.I.F.GFS.P.CQK..PKAKG..EPL.EGLF.LLV...IPTE....SWLSK
Retrocopy DLRGKKGLVYETSVLDPNESIHF*GFSVPGCQKPPPKAKGKKEPLLEGLFQLLVAEQIPTED>KASWLSK

Parental  EWAKRAALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFARAYAQGISRTKYWELIYEDSMDLIAKL
          .WAKR.ALPS.VV.MLDNFPTN..PMSQLSAA.TALNSESN.A.AYA.GI...KY.ELIYED..DLI..L
Retrocopy KWAKRTALPSLVVIMLDNFPTNILPMSQLSAAFTALNSESNTA*AYAEGI---KYRELIYEDCVDLITTL

Parental  P-CVAAKIYRNLYREGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELMRLYLTIHSDHEGGNVSAHTSHLV
          P.CVAAKIY..LY..G...G.IDS.L.W.HNFTNMLGYTD.Q.TELM.LY.TIHSDH...NVSA..S.L.
Retrocopy P<CVAAKIYQYLY*KGKNVGGIDSKLHWPHNFTNMLGYTDAQLTELMHLYHTIHSDHKSSNVSAYISNLL

Parental  GSALSDPYLSFAAAMNGLAGPLHGLA-QEVLVWLTQLQKEVGKDVSDEKLQDYIWNTLN-SGRVVPGYGH
          GSA.S.PYLSFA.AMNGL.GPL..L..Q.VLVWLT.LQKEVGKDV..EKL.DY.WNTLN....V.P.YGH
Retrocopy GSAPSSPYLSFATAMNGLTGPLCVLTNQVVLVWLT*LQKEVGKDVAEEKL*DYTWNTLN>QDEVIPDYGH

Parental  AVLRKTDPRYTCQR-EFALKH-LPNDPMF-KLVAQLYKIVPNVLLEQGKAKNPWPNVD
          .VL.K.DPR.TC...EFALKH...ND.M...LVAQL.KIVPN.LLE.GKAKNPW.NVD
Retrocopy VVLKKIDPRGTCCE<EFALKH<PHNDRML<NLVAQLHKIVPNILLENGKAKNPWSNVD

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	134.52 RPM
SRP007412_cerebellum	0.00 RPM	191.89 RPM
SRP007412_heart	0.00 RPM	225.87 RPM
SRP007412_kidney	0.00 RPM	106.33 RPM
SRP007412_liver	0.00 RPM	40.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2972 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2972 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004371	1 retrocopy	retro_btau_386,
Canis familiaris	ENSCAFG00000000115	1 retrocopy	retro_cfam_765,
Choloepus hoffmanni	ENSCHOG00000000397	1 retrocopy	retro_chof_1803,
Callithrix jacchus	ENSCJAG00000011275	1 retrocopy	retro_cjac_2031,
Dasypus novemcinctus	ENSDNOG00000010907	2 retrocopies	retro_dnov_205, retro_dnov_468,
Echinops telfairi	ENSETEG00000012035	1 retrocopy	retro_etel_584,
Homo sapiens	ENSG00000062485	2 retrocopies	retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla	ENSGGOG00000009096	2 retrocopies	retro_ggor_1432, retro_ggor_2445,
Macropus eugenii	ENSMEUG00000005657	2 retrocopies	retro_meug_1078, retro_meug_1304,
Microcebus murinus	ENSMICG00000017659	2 retrocopies	retro_mmur_1322, retro_mmur_394,
Macaca mulatta	ENSMMUG00000002483	2 retrocopies	retro_mmul_1502, retro_mmul_1840,
Mus musculus	ENSMUSG00000005683	1 retrocopy	retro_mmus_258,
Nomascus leucogenys	ENSNLEG00000017514	2 retrocopies	retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus	ENSOCUG00000007216	1 retrocopy	retro_ocun_1183,
Pongo abelii	ENSPPYG00000004654	1 retrocopy	retro_pabe_2972 ,
Rattus norvegicus	ENSRNOG00000023520	1 retrocopy	retro_rnor_2518,
Sorex araneus	ENSSARG00000010093	2 retrocopies	retro_sara_360, retro_sara_628,
Sus scrofa	ENSSSCG00000021091	1 retrocopy	retro_sscr_321,
Sus scrofa	ENSSSCG00000022858	1 retrocopy	retro_sscr_322,
Tupaia belangeri	ENSTBEG00000006425	1 retrocopy	retro_tbel_4652,
Tarsius syrichta	ENSTSYG00000004483	1 retrocopy	retro_tsyr_1659,