RetrogeneDB ID: retro_pabe_3572

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:10987684..10988837(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGGF1
• Ensembl ID: ENSPPYG00000015574
• Aliases: None
• Description: angiogenic factor with G patch and FHA domains 1 [Source:HGNC Symbol;Acc:24684]

Sequence

>retro_pabe_3572
GAGGAAAAGGATTTGAATTCAGAGGATCCAAAAGCCTTCAGTGTTGAACATACAAGCTGCAATGGGAAAGACAATTTTAC
AAATGTGAAAGAAAGGCCAAAATAGGCATTCATCACAAAAATAATCCCCCAAAAGTCACTGTTCCAATTAGTGGAAATAC
TATGGACTCTCCTTTTAATGAAAACATGTCAATTCAACTTTATTTAAAGATGAGAAAGTCGCAGACAGTGATAGTGAATC
AGAAGAAGGTGAAATCACAGACTCTCAGACCGAGGGTAGTTATGATGAAGACATTACCAGTGAAGGCAATACAACTGCAA
AAGATACTGAAGAGAGAGATGAGGAATAACTGTGGCCCCCATGTATAAGAGTAATTGTCATTAAATCACCCCTGTTACAG
ACAGGATCACTCTTCATCATTACTGCTGTAAAACCTGCTACAATTGAAAGAGAAAATGATATGGAGCATACTCTTCGAAT
CCCTGCAGTTGGTGTCAGTAAGTTTCACGCACAAATTTATTTTGACCATGACTTACAAAGTTGTGTCCTTTTGTATCGGG
CAGTCAAAATGTAACAATTGTTAATGAAAAACGGATTATTCAGCTGAAAACTAAATGTGACCCTTATGTGCTTGAGCATG
GAGATAAAGCAAAAATTGGAGAGACTGTGTTATCTTATTATATTCACCCTGGCAGTAATAGCTATGTTGGATGTGAACCA
GTGCAGGTTAGATCTCACCTTTCCTTGGTAAGAAAGATGAATCATTTGTTGGTCCAACATTAACTAAGAAGGAAAGGAGT
TGGAAAGAAGAAAAGGATTTTAGAAATATATCAGTAAAATATGCTTTACAGAATACAGACTACAAAGATGATAAGATATT
GGAGAATCTAAAATATAAAGATAGAGTTGTAAAACATAAGGAACAGATTGGAAGTGAAGGAAATTTCCAAAGAGATGATG
CTCCTGCATCTGTTCATTCTGAAATTACTGATAGTGACAAAGGTCACAAGATGTTGAAGAAGATATGTTGAAAACATTAG
TAGGCCTGGGGAAGGATGGTGGGAGAATATAAACTCCAATACAGCTTCAACTTTGGCAAACACAAGCAGGATTGGAGACA
GACAAACCATCCTCAATTAAAGAGGCTCACCTT

Alignment

ORF - retro_pabe_3572 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.08 %
• Parental protein coverage: 54.06 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EEKDLNSEDQKTFSVEHTSCSEEENFANMK-KKAKIGIHHKNSPPKVTVPTSGNTIESPLHENIS-KSTS
          EEKDLNSED.K.FSVEHTSC....NF.N.K..KAKIGIHHKN.PPKVTVP.SGNT..SP..EN.S..ST.
Retrocopy EEKDLNSEDPKAFSVEHTSCNGKDNFTNVK<RKAKIGIHHKNNPPKVTVPISGNTMDSPFNENMS<NSTL

Parental  FRDEKIMETDSEPEEGEITDSQTEDSYDEDITSEGNVTAEDSEDEDEDKIWPPCIRVIVIRSPVLQIGSL
          F.DEK....DSE.EEGEITDSQTE.SYDEDITSEGN.TA.D.E..DE...WPPCIRVIVI.SP.LQ.GSL
Retrocopy FKDEKVADSDSESEEGEITDSQTEGSYDEDITSEGNTTAKDTEERDEE*LWPPCIRVIVIKSPLLQTGSL

Parental  FIITAVNPATIGREKDMEHTLRIPEVGVSKFHAEIYFDRDLQSYVLVDQ-GSQNGTIVNGKQILQPKTKC
          FIITAV.PATI.RE.DMEHTLRIP.VGVSKFHA.IYFD.DLQS.VL....GSQN.TIVN.K.I.Q.KTKC
Retrocopy FIITAVKPATIERENDMEHTLRIPAVGVSKFHAQIYFDHDLQSCVLLYR<GSQNVTIVNEKRIIQLKTKC

Parental  DPYVLEHGDEVKIGETVLSFHIHPGSDTCDGCEPGQVRAHLR-LDKKDESFVGPTLSKEEKELERRKELK
          DPYVLEHGD..KIGETVLS..IHPGS....GCEP.QVR.HL..L.KKDESFVGPTL.K.E......K...
Retrocopy DPYVLEHGDKAKIGETVLSYYIHPGSNSYVGCEPVQVRSHLS<LGKKDESFVGPTLTKKERSWKEEKDFR

Parental  KIRVKYGLQNTEYEDEKTLKNPKYKDRAGKRREQVGSEGTFQRDDAPASVHSEITDSNKGRKMLEKMGWK
          .I.VKY.LQNT.Y.D.K.L.N.KYKDR..K..EQ.GSEG.FQRDDAPASVHSEITDS.KG.KML.K...K
Retrocopy NISVKYALQNTDYKDDKILENLKYKDRVVKHKEQIGSEGNFQRDDAPASVHSEITDSDKGHKMLKKIC*K

Parental  KGEGLGK-DGGGMKTPIQLQLRRTHAGLGTGKPSSIEDIHL
          .....G..DGG...TPIQLQL..T.AGL.T.KPSSI...HL
Retrocopy H**AWGR<DGGRI*TPIQLQLWQTQAGLETDKPSSIKEAHL

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	37.04 RPM
SRP007412_cerebellum	0.00 RPM	36.48 RPM
SRP007412_heart	0.00 RPM	11.74 RPM
SRP007412_kidney	0.07 RPM	21.78 RPM
SRP007412_liver	0.00 RPM	13.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3572 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3572 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3572 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000015574	1 retrocopy	retro_pabe_3572 ,
Pan troglodytes	ENSPTRG00000017008	1 retrocopy	retro_ptro_3068,