RetrogeneDB ID: retro_pabe_1420

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16_random:8359430..8360538(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX3
• Ensembl ID: ENSPPYG00000004279
• Aliases: None
• Description: Y box binding protein 3 [Source:HGNC Symbol;Acc:2428]

Sequence

>retro_pabe_1420
AGCGAGGCGGGCGAGGCCACCACCATTACCACCACCCTCCAGCAGGCTCCAGCGGAGGCGGCCGCCGCGGCTCCCCAGGA
CCCGGCGACCAAGAGCCGGGTGGGCAGCGGTGCGCCTCAGGCCGCGACCCGGGAGCCCGCCGCCCTCCTCGCAGGAAACC
CGGGTGGGGACGCGGCCCCCGCAGCCACGGGCACCGCGGCCGCCGCCTCTTTAGCCACCGCCGCGGACAGCGAAGACGCG
AAGAAAAAAGTTCTCGCCACCAAAGTCCTTGGCACTGTCAAATGGTTCAACGTCAGAAATGGATATGGATTTATAAATCT
AAATGACACCAAAGAAGATGTATTTATACATCAGACTGCCAACAAGAAGAATAACCCACGGAAATATCTGCGCAGTGTAG
GAGGTGGAGAAACTATAGAGTTTGATGTGGTTGAGGGAGAGAAGGGTGCAGAAGCAGCCAGTGTGACTGGCCGGGGTGGA
GTTCCTGTGGAAGGCAGTCCTTATGCTGCTGATCGGCGCAGTTACAGACGTGGTTACTATGGAAGGCGCCATGGCCCTCC
CCGGAATTACGCTGGGAGGAGGAGGAAGAAGGGAGCGGCAGCAGTGAAGGATTTGACCCCCCTATCACTGATAGGCAGTT
CTCTGGGGCCCGGAATCGGCTGCGCCGCCCCCAGTATCGCCCTCAGTACAGGCAGCAGCGGTTCCCGCCTTACCACGTGG
GACAGATGTTTGACCGTCGCTCACCTTCTTACCCCATCCCAACAGAATACAGGCTGTTGAGATTGGAGAGATAAAGGATG
GAGTCCCAGAAGGAGCACAACTTCAGAGACCAGTTCATTGAAATTCAACTTACCGCCCAAGGTACCGTAGCAGGGGACCT
CCTCGCCCACGACCTGCCCCAGCAGTTGGAGAGGCTGAAGATAAAGAAAATCAGCAAGCCTCCAGTGGTCCAAACCAGCC
GCCTGTTCGCCGTGGATACCGGCGTCCCTACAATTACGGGCGTCGCCCACGGCCTCCTAACGCTCCTTCGCAAGATGGCA
AAGAGGCCAAGGCAGGTGAAGCACGAAGTGAGAACCCTGCTCCATCCACCGAGCAGAGTAGTGCTGAG

Alignment

ORF - retro_pabe_1420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.17 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SEAGEATTTTTTLPQAPTEAAAAAPQDPAPKSPVGSGAPQAAAPAPAAHVAGNPGGDAAPAATGTAAAAS
          SEAGEATT.TTTL.QAP.EAAAAAPQDPA.KS.VGSGAPQAA...PAA..AGNPGGDAAPAATGTAAAAS
Retrocopy SEAGEATTITTTLQQAPAEAAAAAPQDPATKSRVGSGAPQAATREPAALLAGNPGGDAAPAATGTAAAAS

Parental  LATAAGSEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVE
          LATAA.SEDA.KKVLATKVLGTVKWFNVRNGYGFIN.NDTKEDVF.HQTA.KKNNPRKYLRSVG.GET.E
Retrocopy LATAADSEDAKKKVLATKVLGTVKWFNVRNGYGFINLNDTKEDVFIHQTANKKNNPRKYLRSVGGGETIE

Parental  FDVVEGEKGAEAANVTGPDGVPVEGSRYAADRRRYRRGYYGRRRGPPRNYAG-EEEEEGSGSSEGFDPPA
          FDVVEGEKGAEAA.VTG..GVPVEGS.YAADRR.YRRGYYGRR.GPPRNYAG.EEEEEGSGSSEGFDPP.
Retrocopy FDVVEGEKGAEAASVTGRGGVPVEGSPYAADRRSYRRGYYGRRHGPPRNYAG<EEEEEGSGSSEGFDPPI

Parental  TDRQFSGARNQLRRPQYRPQYRQRRFPPYHVGQTFDRRS-RVLPHPNRIQAGEIGEMKDGVPEGAQLQGP
          TDRQFSGARN.LRRPQYRPQYRQ.RFPPYHVGQ.FDRRS...LPHPNRIQA.EIGE.KDGVPEGAQLQ.P
Retrocopy TDRQFSGARNRLRRPQYRPQYRQQRFPPYHVGQMFDRRS<TFLPHPNRIQAVEIGEIKDGVPEGAQLQRP

Parental  VHRNPTYRPRYRSRGPPRPRPAPAVGEAEDKENQQATSGPNQQSVRRGYRRPYNYRRRPRPPNAPSQDGK
          VH.N.TYRPRYRSRGPPRPRPAPAVGEAEDKENQQA.SGPNQ..VRRGYRRPYNY.RRPRPPNAPSQDGK
Retrocopy VH*NSTYRPRYRSRGPPRPRPAPAVGEAEDKENQQASSGPNQPPVRRGYRRPYNYGRRPRPPNAPSQDGK

Parental  EAKAGEAPTENPAPPTQQSSAE
          EAKAGEA..ENPAP.T.QSSAE
Retrocopy EAKAGEARSENPAPSTEQSSAE

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	0.33 RPM	16.37 RPM
SRP007412_cerebellum	0.00 RPM	6.57 RPM
SRP007412_heart	0.00 RPM	172.46 RPM
SRP007412_kidney	0.07 RPM	82.04 RPM
SRP007412_liver	0.00 RPM	84.22 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1420 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1420 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1420 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000060138	1 retrocopy	retro_hsap_1674,
Pongo abelii	ENSPPYG00000001466	7 retrocopies	retro_pabe_1216, retro_pabe_1320, retro_pabe_2054, retro_pabe_2292, retro_pabe_3167, retro_pabe_3388, retro_pabe_3502,
Pongo abelii	ENSPPYG00000004279	1 retrocopy	retro_pabe_1420 ,
Tupaia belangeri	ENSTBEG00000012570	1 retrocopy	retro_tbel_996,