RetrogeneDB ID: retro_pabe_3391

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:26670853..26671590(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSPPYG00000012663
• Aliases: None
• Description: 14-3-3 protein theta [Source:UniProtKB/Swiss-Prot;Acc:Q5RFJ2]

Sequence

>retro_pabe_3391
ATGGATAAAAATGAGCTGGTTCAGAAGGCCAAACTGGCCGAGCAGGCTGAGTGATATGATGACATGGCAGCCTGCATGAA
GTCTGTAACTGAGCAAGGAGCTTAATTATCAAATGAGGAGAGGAATCTTCTCTCAGTTGCTTATAAAAATGTTGTAGGAG
CCCGTAGGTCATCTTGGAGCGTCGTCTCAAGTATTGAACAAAAGACGAAATGTGCTGAGAAAAAAAATAGCAGATGGCTC
AAGAATACAGAGAGAAAACTGAGACCGAGCTAAGAGATAGCGGCAATGATGTACTGTCTCTTTTGGAAAAGTTCTTGATC
CCCAATGCTTCACAAGCGAGAGCAAATTCTTCTATTTGAAAATGAAAGGAGATCACTACCGTTACTTGGCTGAGGTTGCC
GCTGGTGATGACAAGAAAGGGATTGTGGATCAGTCACAACAAGCATACCAAGAAGCTTTTGAAATCAGCAAGAAGGAAAT
GCAACCAACATATCCGATCAGACTGGGTCTGGCCCTTAACTTCTCCGTGTTCTATTATGACGTTCTGAATTCCCCCAGAG
AAAGCCTGCTCTCTTGCAAAGACAGCTTTTGATGAAGCCATTGCTGAACTTGATACATTAAGTGAAGAGTCATCCAAAGA
CAGCACGCTAATAATGCAATTACTGAGTGACAACTTGACATTGTGGACATCGGATACCCAAGGAGACGAAGCTGAAGCAG
GAGAAGGAGGGGAAAAT

Alignment

ORF - retro_pabe_3391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEKTELIQKAKLAEQAERYDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTD
          M.K.EL.QKAKLAEQAE.YDDMA.CMK.VTEQGA.LSNEERNLLSVAYKNVVG.RRS.W.V.SSIEQKT.
Retrocopy MDKNELVQKAKLAEQAE*YDDMAACMKSVTEQGA*LSNEERNLLSVAYKNVVGARRSSWSVVSSIEQKTK

Parental  TSDKKL-QLIKDYREKV-ESELRSICTTVLELLDKYLIANAT-NPESKVFYLKMKGDYFRYLAEVACGDD
          ..........K....K..E.ELR.....VL.LL.K.LI.NA....ESK.FYLKMKGD..RYLAEVA.GDD
Retrocopy CAEXXXSRWLKNTERKL<ETELRDSGNDVLSLLEKFLIPNAS<TSESKFFYLKMKGDHYRYLAEVAAGDD

Parental  RKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNN-PELACTLAKTAFDEAIAELDTL
          .K...D.SQ.AYQEAF.ISKKEMQPT.PIRLGLALNFSVFYY..LN..PE.AC.LAKTAFDEAIAELDTL
Retrocopy KKGIVDQSQQAYQEAFEISKKEMQPTYPIRLGLALNFSVFYYDVLNS>PEKACSLAKTAFDEAIAELDTL

Parental  NEDSYKDSTLIMQLLRDNLTLWTSDSAGEECDAAEGAEN
          .E.S.KDSTLIMQLL.DNLTLWTSD..G.E..A.EG.EN
Retrocopy SEESSKDSTLIMQLLSDNLTLWTSDTQGDEAEAGEGGEN

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	98.14 RPM
SRP007412_cerebellum	0.00 RPM	198.82 RPM
SRP007412_heart	0.00 RPM	44.76 RPM
SRP007412_kidney	0.00 RPM	53.73 RPM
SRP007412_liver	0.00 RPM	27.88 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3391 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3391 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3391 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2887

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002108	2 retrocopies	retro_btau_1180, retro_btau_86,
Callithrix jacchus	ENSCJAG00000006394	2 retrocopies	retro_cjac_2197, retro_cjac_3127,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Homo sapiens	ENSG00000134308	2 retrocopies	retro_hsap_3004, retro_hsap_8,
Gorilla gorilla	ENSGGOG00000001569	1 retrocopy	retro_ggor_2081,
Macropus eugenii	ENSMEUG00000014442	7 retrocopies	retro_meug_1122, retro_meug_1208, retro_meug_1259, retro_meug_1549, retro_meug_1918, retro_meug_2106, retro_meug_538,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Mustela putorius furo	ENSMPUG00000013252	2 retrocopies	retro_mputfur_1132, retro_mputfur_730,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463,
Pongo abelii	ENSPPYG00000007769	4 retrocopies	retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,
Pongo abelii	ENSPPYG00000011041	5 retrocopies	retro_pabe_3453, retro_pabe_3454, retro_pabe_3519, retro_pabe_3520, retro_pabe_692,
Pongo abelii	ENSPPYG00000012663	4 retrocopies	retro_pabe_1165, retro_pabe_2490, retro_pabe_3391 , retro_pabe_3511,
Pongo abelii	ENSPPYG00000018791	7 retrocopies	retro_pabe_103, retro_pabe_1242, retro_pabe_2047, retro_pabe_3417, retro_pabe_3740, retro_pabe_556, retro_pabe_89,
Pelodiscus sinensis	ENSPSIG00000012692	1 retrocopy	retro_psin_2,
Pan troglodytes	ENSPTRG00000011641	2 retrocopies	retro_ptro_2032, retro_ptro_3,
Pteropus vampyrus	ENSPVAG00000005334	1 retrocopy	retro_pvam_983,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,