RetrogeneDB ID: retro_pabe_3256

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:52103774..52104447(+)
• Located in intron of: ENSPPYG00000018580

Retrocopy information

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

Parental gene information

• Parental gene symbol: F3
• Ensembl ID: ENSPPYG00000001139
• Aliases: None
• Description: tissue factor precursor [Source:RefSeq peptide;Acc:NP_001126163]

Sequence

>retro_pabe_3256
CTGGCGACTCCAGCCTGGGCCTGGGTCCCACGTCCTGAGACTGCCTTAGCTCAGATTCTCCTGCTCCGCTAGGTCCTCCT
CAAGGCGGCTAGTGCTTCTGGCACTGCAGATAGAGTGGTAGCATATAATGTGTAATCAACGAATTTCAAGACAATTTTGG
AGCTGGAACCCAAGCCTATCATCAATCATGTCTACACTGCCCAGACAAGCTCTGCATCAGGAGACTGGAAAAGCCATGCT
TGGAAACCCCGGACACAGAGAGTGACCTCACAGATGGGACAGCAAGGACGTGATACAGTCGTCCTCGGCCCAGGGCCCTT
CCTGCCCCGCTGGGGATGCAGCCACCAAGGGTTCTGCCGGGAACCTCTGATCCGAAGCTCCCCAGAGTTTACACGTGACC
TGGAGAAACACCTGGGACAGCCAGCAATTCAGTGTTTTGAATCAGTCAGGACAAAACAACGTGACAGTATCAGAATGACG
TACCTTAGAAAGAATGACATATTCCTAGGCCTCTGGGAGTTTGCGACAAGTACTCAAGTTGTACACTTTATTATTGGAAA
GCTTCATGTACGGGAAAGAAAACAGCCAAGACAAACACAAATGCGTTTTTGATGGATATGGATAAAGGGGAAACCACCGT
TCCAGTGTTCAGTGATTCCATCCGAAGACTACA

Alignment

ORF - retro_pabe_3256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.32 %
• Parental protein coverage: 77.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  METPAWPRVPRPETAVAWTLLLGWVFAQVAGASGTTNTVAAYNLTWKSTNFKTILEWEPKPL-NQVYTVQ
          ..TPAW..VPRPETA.A..LLL..V....A.ASGT...V.AYN....STNFKTILE.EPKP..N.VYT.Q
Retrocopy LATPAWAWVPRPETALAQILLLR*VLLKAASASGTADRVVAYNV*--STNFKTILELEPKPIINHVYTAQ

Parental  ISTKTGDWKSK-CFYTADTECDLTDEIV-KDVKQTYLARVFSYPAGNVGSTGSAG-EPLYENSPEFTPYL
          .S...GDWKS..C..T.DTE.DLTD....KDV.Q...A...S.PAG.....GSAG.EPL...SPEFT..L
Retrocopy TSSASGDWKSH<CLETPDTESDLTDGTA<KDVIQSSSAQGPSCPAGDAATKGSAG<EPLIRSSPEFTRDL

Parental  ETNLGQPTIQSFEQVGTKVNVTVQDERTLVRRNNTFLSLRD-VFGKDLIYTLYYWKSSSSGKKTAKTNTN
          E..LGQP.IQ.FE.V.TK.........T..R.N..FL.L...V..K....TLYYWK.S..GKKTAKTNTN
Retrocopy EKHLGQPAIQCFESVRTKQRDSIR--MTYLRKNDIFLGLWE<VCDKYSSCTLYYWKASCTGKKTAKTNTN

Parental  EFLIDVDKGE-NYCFSVQAVIPSRT
          .FL.D.DKGE.N...SVQ...P..T
Retrocopy AFLMDMDKGE<NHRSSVQ*FHPKTT

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	13.99 RPM
SRP007412_cerebellum	0.00 RPM	2.80 RPM
SRP007412_heart	0.00 RPM	11.23 RPM
SRP007412_kidney	0.00 RPM	10.64 RPM
SRP007412_liver	0.00 RPM	1.81 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3256 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3256 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3952
Gorilla gorilla	retro_ggor_2655

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000117525	1 retrocopy	retro_hsap_3952,
Gorilla gorilla	ENSGGOG00000014683	1 retrocopy	retro_ggor_2655,
Nomascus leucogenys	ENSNLEG00000011112	1 retrocopy	retro_nleu_531,
Pongo abelii	ENSPPYG00000001139	2 retrocopies	retro_pabe_3255, retro_pabe_3256 ,