RetrogeneDB ID: retro_pabe_828

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:25634225..25635357(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000004364
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KNOP1
• Ensembl ID: ENSPPYG00000007151
• Aliases: None
• Description: lysine-rich nucleolar protein 1 [Source:HGNC Symbol;Acc:34404]

Sequence

>retro_pabe_828
CCTGGGATCCCAGAGAAGAAAAAGAAGAAGAAAGTGGTCAAAGAACCAGAGACTCAATACTCAATTTTAAACAATGATGA
TTACTTTGCCCATGTTTCTCCTATAAAAGCCACAGTCCCCTCTAAGAGTGTGGTCCACAGGCAGGCACCTGAAATGCCTC
TAGTGAAGAAAAAGAAGAAAGAGAAGGCTGTCAGCACCCTTTGCGAGGAGCACGTAGAACCTGAGACCACGCTGCGTGCC
AGACGGACAGAGAAGTCATCCAGCCCAAGGAATCAGGTGCTTGGCTACTTGGAGTTCCTCAGTGGGCAGAAGAAAAAGAA
GAAGTCATCTCTCGCCATGTCCCATGCCTCTGGGGTGAAAATCTCCCCAGAACCCAGACAGGGTGAGGAAGAAAACAGAG
TTGGCAAGAAGCTTAAAAAACATAAGAAGGAAAAAAAGAGGGCCCAGGACTCCACAGCTTTCTCAGTCCAGGACCCTTGG
TTCTGCGAGGTCGGGGATGCTGTGGACACTTGCTCAGTGGGGAAGGAGGGTGAGGAACAGGTAGCCTTGGGGCAGAAGTG
GAGGCACAAGAGCCCCAGGGAACACAGTGGGAAGGTGAAGAAGAAAAAAAAAAATCCACCAGGAGGGAGACGCCCTCCCA
GGCCACTCCAAGCCCTCCAGGTCCATGGAGAGCTGCCCTAGGAAACGAAGTAAAAAGAAGCCAGTCAAAGTGGAGGCTCC
GGAATACATCCCCATAGGAGATGGCCCTAAGGCCCCCGCGAAGTAAAAGATGAAGTCCAAGAAGAAGGTAAAGCAGCCAG
TCATTGAGGAGCTGGCTCTGAAAAGGAAGAAAAAGAAAAGGAAAGGGAGTAGGGTAGCAGGAGAGCCTTGGAAGGAGGAA
ACAGACACGGACTTGGAGGTGGTGTTGGAAAAGAAAGGCAACATGGACTAGCCGCACATAGACCAGGTGAGGCGAAAAGC
CTTGCAAGAAGAGACTGATCGCGAGTCAGGCAAAACGGAAGCTTCTGAAACCAGGAAGTGGACGGGAACCCGGTTTGGCC
AGTGGGATACTGCTGGTTTTGAGAACAAGGAACAGAAACTGAAATTTCTCAAACTTATGGGTGGCTTCAAAAACTTGTCC
CCTTCGATTAGC

Alignment

ORF - retro_pabe_828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.98 %
• Parental protein coverage: 74.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGLPEKKKKKKVVKEPETRYSVLN-DDYFADISPVRATSPSKSVAHGQAPEMPLVKKKKKKKKGVSTLCE
          PG.PEKKKKKKVVKEPET.YS.LN.DDYFA..SP..AT.PSKSV.H.QAPEMPLVKKKKK.K..VSTLCE
Retrocopy PGIPEKKKKKKVVKEPETQYSILNNDDYFAHVSPIKATVPSKSVVHRQAPEMPLVKKKKKEK-AVSTLCE

Parental  EHVEPETTLPARRTEKSPSSRKQVLGHLEFLSGEKKKKKSPLAMSHASGVKTSADPRQGEEETRVGKKLK
          EHVEPETTL.ARRTEKS.S.R.QVLG.LEFLSG.KKKKKS.LAMSHASGVK.S..PRQGEEE.RVGKKLK
Retrocopy EHVEPETTLRARRTEKSSSPRNQVLGYLEFLSGQKKKKKSSLAMSHASGVKISPEPRQGEEENRVGKKLK

Parental  KHKKEKKGAQDPTAFSVQDPWFCEAREARDVGDTCSVGKKDEEQAALGQKRKRKSPREHNGKVKK-KKKI
          KHKKEKK.AQD.TAFSVQDPWFCE...A.D...TCSVGK..EEQ.ALGQK...KSPREH.GKVKK.....
Retrocopy KHKKEKKRAQDSTAFSVQDPWFCEVGDAVD---TCSVGKEGEEQVALGQKWRHKSPREHSGKVKK>XXXX

Parental  HQEGDALPGHSKTSRSMESSPRKGSKKKPVKVEAPEYIPISDDPKASTKKKMKSKKKVEQPVIEEPALKR
          HQEGDALPGHSK.SRSMES.PRK.SKKKPVKVEAPEYIPI.D.PKA..K.KMKSKKKV.QPVIEE.ALKR
Retrocopy HQEGDALPGHSKPSRSMESCPRKRSKKKPVKVEAPEYIPIGDGPKAPAK*KMKSKKKVKQPVIEELALKR

Parental  KKKKKRKESGVAGDPWKEETDTDLEVVLEKKGNMDEAHIDQVRRKALQEEIDRESGKTEASETRKWTGTH
          .KKKKRK.S.VAG.PWKEETDTDLEVVLEKKGNMD..HIDQVRRKALQEE.DRESGKTEASETRKWTGT.
Retrocopy -KKKKRKGSRVAGEPWKEETDTDLEVVLEKKGNMD*PHIDQVRRKALQEETDRESGKTEASETRKWTGTR

Parental  F-QWDTAGFENEDQKLKFLRLMGGFKNLSPSFS
          F.QWDTAGFEN..QKLKFL.LMGGFKNLSPS.S
Retrocopy FGQWDTAGFENKEQKLKFLKLMGGFKNLSPSIS

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	4.92 RPM
SRP007412_cerebellum	0.00 RPM	8.76 RPM
SRP007412_heart	0.09 RPM	3.16 RPM
SRP007412_kidney	0.03 RPM	6.86 RPM
SRP007412_liver	0.12 RPM	6.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_828 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_828 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_828 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_979
Pan troglodytes	retro_ptro_767

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018032	2 retrocopies	retro_cfam_1557, retro_cfam_1763,
Callithrix jacchus	ENSCJAG00000009625	1 retrocopy	retro_cjac_3199,
Homo sapiens	ENSG00000103550	3 retrocopies	retro_hsap_3487, retro_hsap_4007, retro_hsap_979,
Gorilla gorilla	ENSGGOG00000005673	1 retrocopy	retro_ggor_2691,
Macaca mulatta	ENSMMUG00000002707	2 retrocopies	retro_mmul_1771, retro_mmul_798,
Nomascus leucogenys	ENSNLEG00000012496	2 retrocopies	retro_nleu_1618, retro_nleu_551,
Otolemur garnettii	ENSOGAG00000010065	4 retrocopies	retro_ogar_1115, retro_ogar_1480, retro_ogar_1481, retro_ogar_2259,
Pongo abelii	ENSPPYG00000007151	3 retrocopies	retro_pabe_3293, retro_pabe_828 , retro_pabe_920,
Pan troglodytes	ENSPTRG00000007836	3 retrocopies	retro_ptro_2360, retro_ptro_767, retro_ptro_924,