RetrogeneDB ID: retro_pabe_3809

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:124534264..124535273(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBLIM1
• Ensembl ID: ENSPPYG00000001837
• Aliases: None
• Description: filamin-binding LIM protein 1 [Source:RefSeq peptide;Acc:NP_001127194]

Sequence

>retro_pabe_3809
ATGGCCTCAAAGCCTGAGAAGAGTGTGGCATCGTCTGTCTTTATCACCCTTGCACCCCTGTGCCGCGATTTAGCTGTGGT
TGAGGAAGGGAGGCAGGCGGTTTGTGAGGCCTGATGTGGCCTCCCCTGGGAGGCTCCTGCCCCCATGAAGGCACCCGGAG
CTGGCTTAGCGGGAGAGCCCAGCCCCTGGGCACCCCCTGGCAGGGCTTCAGCCACAGTGCCAGCTGCACCTCTGCAGCTC
TCCAATGGAGGATGCTCACCCCCTCCTCCTGTCCTGGATGGTGAGGACGCACTTCCTGACCTGGACCTCGTCCCACCCCC
TCCACTGCCCTCTCCGGTGCTCCTGTCTTCTGAAGAAGAGGCTCCTGCTCCAATGGGTGCCTCACTCATTGCAGACTTAG
AGCAGTGGCACCTGCCCTCACCCCCACCCCGACCACAGGCCCCGGCGGAGGGACCTTCAGTCCAGCCTGGCTCCAGTCCC
CTCAGGCCTGGGGAGGAAGAGCTTTCGCCTTCCCCAGCAGAGCCTGTTGAGAGAGTCATCCACAGACATCTGTGCCTTCT
GCCACAAAACCGTGTCCCCCCAATAGCTGGCTGTGGAGGCCATGAAGAGGCAGTACCACGCCCAGTGCTTCACGTGGCAC
ACCTGCCGCCGCCAGCTGGCTGGGCAGAGCTTCTACCAGGATGGGTGACCCCTCTGCGAACCCTGCTACCAGGACACGCT
GGAGAAGTGTGGCAAGTGTGGCGAGGTGGTCCGGGAGCACATCATCAGGGCCCTGGGCCAGGCCTTCCACCCCTGCTTCT
TCATGTGTGTGACCTGTGCCCGGTGCATCCAGGATGAGAGCTTTGCCCTGGGCAGCCAAAACGAGATGTACTGCCTAGAC
GAATTCTACAAGAAATTCACCCCCGTATGCAGCATCTGTGAGAATCCCATTATTCTTCGGGATGGGAAAGATGCCTTCAA
AATCAAGTGCATGGGAAGAAACTTCCATGTAAATTGCTACAGGTGTGAG

Alignment

ORF - retro_pabe_3809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASKPEKRVASSVFITLAPPRRDVAVAEEVRQAVCEARRGRPWEAPAPMKTPEAGLEGRPSPWTPPGRAA
          MASKPEK.VASSVFITLAP..RD.AV.EE.RQAVCEA..G.PWEAPAPMK.P.AGL.G.PSPW.PPGRA.
Retrocopy MASKPEKSVASSVFITLAPLCRDLAVVEEGRQAVCEA*CGLPWEAPAPMKAPGAGLAGEPSPWAPPGRAS

Parental  ATVPAAPMQLSNGGCPPPPPVLDGEDALPDLDLLPPPPPPPPVLLPSEEEAPASMGASLIADLEQLHLSP
          ATVPAAP.QLSNGGC.PPPPVLDGEDALPDLDL.PPPP.P.PVLL.SEEEAPA.MGASLIADLEQ.HL..
Retrocopy ATVPAAPLQLSNGGCSPPPPVLDGEDALPDLDLVPPPPLPSPVLLSSEEEAPAPMGASLIADLEQWHL--

Parental  PLPPPPPQAPAERPSVQP--SPLRPVEEELPPP-PAERVEKGASTDICAFCHKTVSPRELAVEAMKRQYH
          P.PPP.PQAPAE.PSVQP..SPLRP..EE...P.P........STDICAFCHKTVSP..LAVEAMKRQYH
Retrocopy PSPPPRPQAPAEGPSVQPGSSPLRP-GEEELSP>PQQSLLRESSTDICAFCHKTVSPQ*LAVEAMKRQYH

Parental  AQCFTCRTCRRQLAGQSFYQKDGRPLCEPCYQDTLERCGKCGEVVRDHIIRALGQAFHPSCFTCVTCARC
          AQCFT..TCRRQLAGQSFYQ.DG.PLCEPCYQDTLE.CGKCGEVVR.HIIRALGQAFHP..F.CVTCARC
Retrocopy AQCFTWHTCRRQLAGQSFYQ-DG*PLCEPCYQDTLEKCGKCGEVVREHIIRALGQAFHPCFFMCVTCARC

Parental  IGDESFALGSQNEVYCLDDFYRKFAPVCSICENPIIPRDGKDAFKIECMGRSFHENCYRCE
          I.DESFALGSQNE.YCLD.FY.KF.PVCSICENPII.RDGKDAFKI.CMGR.FH.NCYRCE
Retrocopy IQDESFALGSQNEMYCLDEFYKKFTPVCSICENPIILRDGKDAFKIKCMGRNFHVNCYRCE

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	4.15 RPM
SRP007412_cerebellum	0.00 RPM	0.85 RPM
SRP007412_heart	0.03 RPM	8.37 RPM
SRP007412_kidney	0.07 RPM	5.80 RPM
SRP007412_liver	0.00 RPM	2.72 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3809 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3809 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3809 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4898
Pan troglodytes	retro_ptro_3266
Gorilla gorilla	retro_ggor_3058
Macaca mulatta	retro_mmul_2635

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018725	1 retrocopy	retro_btau_1013,
Homo sapiens	ENSG00000162458	2 retrocopies	retro_hsap_4898, retro_hsap_778,
Gorilla gorilla	ENSGGOG00000015190	2 retrocopies	retro_ggor_3058, retro_ggor_645,
Macaca mulatta	ENSMMUG00000032243	2 retrocopies	retro_mmul_1095, retro_mmul_2635,
Pongo abelii	ENSPPYG00000001837	2 retrocopies	retro_pabe_3809 , retro_pabe_751,
Pan troglodytes	ENSPTRG00000000208	2 retrocopies	retro_ptro_3266, retro_ptro_544,
Pteropus vampyrus	ENSPVAG00000009000	1 retrocopy	retro_pvam_415,