RetrogeneDB ID: retro_pabe_1321

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:85645343..85646064(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA2
• Ensembl ID: ENSPPYG00000017933
• Aliases: None
• Description: F-actin-capping protein subunit alpha-2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R4P6]

Sequence

>retro_pabe_1321
AGGGAAAAAGCAGCCCGTGCATCTGCACAGTATAACTTGGAGCAGTTTACTCCTGTAAAAATGGAAGGTTATTAAGATCA
GGTATTGATAACAAAACATGGCGACTTGGGAAATGGAAAGTTTTAGGATCCAAAGAACAGAATCTGTTTTAAATTTGGTC
ACTTCAGAAACGAGGCAACTGATCCAAGACCCTGTGAAGTAGAAAATGCAATTGAATCATGGAGAACTTCAGTAGAAACT
ACTCTGCGAGCTTACGTAAAAGAACATTACCCGAATGGAGTCTGCACTGTGTATAGCAAAAAAAATAGATGGACAGTAAA
CCACTATTGCATGCATAGAAAGCCATCAGTTCCAAGCAAAAAACTTTTGGAATGGTCGTTGGAGGTCAGAGTAGAGGTTT
ATAATCACTCCTTCAACCACTCAAGTGGTTGGCATCTTGAAAATTCAGGTTCATTATTATGAAGACAGTAATGTTCAGCT
AGTGAGTCATAAAGATATACAAGATTCCCTAACAGTGTCTAATGAAGTGCAAACAGCAAAAGAATTTACAAAGATTGTAG
AAGCTGCAGAAAATGAATACCAGACTGCCATCAGGGAGAATTATCAGACAATGTCGGACACTACTTTCAAAGCCTTACAT
CGACAATTGCCACTTACACGCACTAAGATTGATTGGAACAAGATCTTTAGCTACGAGATTGGCAAACAGATGCAGAATGC
A

Alignment

ORF - retro_pabe_1321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.14 %
• Parental protein coverage: 83.92 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  REGAAHAFAQYNLDQFTPVKIEGYEDQVLITEHGDLGNGKFLDPKNRICFKFDHLRKEATDPRPCEVENA
          RE.AA.A.AQYNL.QFTPVK.EGY.DQVLIT.HGDLGNGKF.DPKNRICFKF.H.R.EATDPRPCEVENA
Retrocopy REKAARASAQYNLEQFTPVKMEGY*DQVLITKHGDLGNGKF*DPKNRICFKFGHFRNEATDPRPCEVENA

Parental  VESWRTSVETALRAYVKEHYPNGVCTVYGKKI-DGQQTIIACIESHQFQAKNFWNGRWRSEWKFTITPST
          .ESWRTSVET.LRAYVKEHYPNGVCTVY.....DGQ.T.IACIESHQFQAKNFWNGRWRSE..F.ITPST
Retrocopy IESWRTSVETTLRAYVKEHYPNGVCTVYSXXX>DGQ*TTIACIESHQFQAKNFWNGRWRSE*RFIITPST

Parental  TQVVGILKIQVHYYEDGNVQLVSHKDIQDSLTVSNEVQTAKEFIKIVEAAENEYQTAISENYQTMSDTTF
          TQVVGILKIQVHYYED.NVQLVSHKDIQDSLTVSNEVQTAKEF.KIVEAAENEYQTAI.ENYQTMSDTTF
Retrocopy TQVVGILKIQVHYYEDSNVQLVSHKDIQDSLTVSNEVQTAKEFTKIVEAAENEYQTAIRENYQTMSDTTF

Parental  KALRRQLPVTRTKIDWNKILSYKIGKEMQNA
          KAL.RQLP.TRTKIDWNKI.SY.IGK.MQNA
Retrocopy KALHRQLPLTRTKIDWNKIFSYEIGKQMQNA

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	0.17 RPM	44.95 RPM
SRP007412_cerebellum	0.00 RPM	40.86 RPM
SRP007412_heart	0.06 RPM	61.74 RPM
SRP007412_kidney	0.00 RPM	41.04 RPM
SRP007412_liver	0.03 RPM	27.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1321 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1321 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1321 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004925	2 retrocopies	retro_chof_2296, retro_chof_680,
Cavia porcellus	ENSCPOG00000007677	1 retrocopy	retro_cpor_205,
Dasypus novemcinctus	ENSDNOG00000005771	1 retrocopy	retro_dnov_1892,
Dipodomys ordii	ENSDORG00000016226	1 retrocopy	retro_dord_266,
Erinaceus europaeus	ENSEEUG00000009063	5 retrocopies	retro_eeur_142, retro_eeur_167, retro_eeur_351, retro_eeur_365, retro_eeur_482,
Echinops telfairi	ENSETEG00000019711	3 retrocopies	retro_etel_1516, retro_etel_2020, retro_etel_442,
Gorilla gorilla	ENSGGOG00000012158	1 retrocopy	retro_ggor_1774,
Microcebus murinus	ENSMICG00000000707	1 retrocopy	retro_mmur_1224,
Myotis lucifugus	ENSMLUG00000007910	1 retrocopy	retro_mluc_2595,
Oryctolagus cuniculus	ENSOCUG00000003591	2 retrocopies	retro_ocun_1531, retro_ocun_873,
Pongo abelii	ENSPPYG00000001021	2 retrocopies	retro_pabe_2116, retro_pabe_3789,
Pongo abelii	ENSPPYG00000017933	1 retrocopy	retro_pabe_1321 ,
Sus scrofa	ENSSSCG00000026942	2 retrocopies	retro_sscr_1127, retro_sscr_600,
Ictidomys tridecemlineatus	ENSSTOG00000024828	1 retrocopy	retro_itri_1561,
Tupaia belangeri	ENSTBEG00000012657	2 retrocopies	retro_tbel_2004, retro_tbel_2228,