RetrogeneDB ID: retro_pabe_3300

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:14993138..14993633(-)
• Located in intron of: ENSPPYG00000018379

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLTA
• Ensembl ID: ENSPPYG00000019069
• Aliases: None
• Description: clathrin, light chain A [Source:HGNC Symbol;Acc:2090]

Sequence

>retro_pabe_3300
ATGGCTGAGCAAGATCCATTCGGTGTCCCTGCTGGCACCCCTGGGGATCCCGTCCTGGAGAACAGAGTGGCTGCCACCAG
TGAAGAAGACCCAGCTGCAGCCTCTTGGCACAGCAAGAGAGCAAGACTACGGGTATCAAGAAAAACAAGGTCGCCTTTGA
CATCCTGGATGGTGTCACCCCCAGGCCCCAGCCACAAGGTGAACAGCTGGGAGTCCAGATGCTGTTGACGGAGTGATGAT
GGTGACTACTACCAGGAAAGTAATGGTCCAAGAGACAATTATGCAGCTATTTCACAAGTGGATCGATTCCAGTCACAGCC
TGAAAATATCTGCAGATGGAAAGAAGAGAAAACGGAATGCTTAGAAGCCCTTGCTGCCTATTCTCAGAAGCAAGAAGCAG
AGTGGAAAGAAAAAGCAATAAATGAGCTAGAAGAGTGGTGTGCAAGACAAGACGAGCAGCTACAGAAAAGAAAGGCAAAC
AACAGGGCAGAAGAT

Alignment

ORF - retro_pabe_3300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.41 %
• Parental protein coverage: 66.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAELDPFGAPAGAPGGPALGNGVAGAGEEDPAAA-FLAQQESEIAGIE-NDEAFAILDGGAPGPQPHGEP
          MAE.DPFG.PAG.PG.P.L.N.VA...EEDPAAA..LAQQES...GI..N..AF.ILDG..P.PQP.GE.
Retrocopy MAEQDPFGVPAGTPGDPVLENRVAATSEEDPAAA<LLAQQESKTTGIKKNKVAFDILDGVTPRPQPQGEQ

Parental  -PGGPDAVDGVM-NGEYYQESNGPTDSYAAISQVDRLQSEPESIRKWREEQMERLEALDANSRKQEAEWK
          ..G.PDAVDGVM..G.YYQESNGP.D.YAAISQVDR.QS.PE.I..W.EE..E.LEAL.A.S.KQEAEWK
Retrocopy <AGSPDAVDGVM<DGDYYQESNGPRDNYAAISQVDRFQSQPENICRWKEEKTECLEALAAYSQKQEAEWK

Parental  EKAIKELEEWYARQDEQLQKTKANNRVAD
          EKAI.ELEEW.ARQDEQLQK.KANNR..D
Retrocopy EKAINELEEWCARQDEQLQKRKANNRAED

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	95.98 RPM
SRP007412_cerebellum	0.00 RPM	91.57 RPM
SRP007412_heart	0.03 RPM	19.66 RPM
SRP007412_kidney	0.03 RPM	87.77 RPM
SRP007412_liver	0.00 RPM	52.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3300 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3300 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001137	1 retrocopy	retro_btau_327,
Homo sapiens	ENSG00000122705	2 retrocopies	retro_hsap_4022, retro_hsap_955,
Macropus eugenii	ENSMEUG00000010858	1 retrocopy	retro_meug_480,
Macaca mulatta	ENSMMUG00000006132	2 retrocopies	retro_mmul_2319, retro_mmul_785,
Monodelphis domestica	ENSMODG00000002610	1 retrocopy	retro_mdom_1148,
Nomascus leucogenys	ENSNLEG00000003874	1 retrocopy	retro_nleu_659,
Pongo abelii	ENSPPYG00000019069	1 retrocopy	retro_pabe_3300 ,
Pan troglodytes	ENSPTRG00000020930	1 retrocopy	retro_ptro_2727,