RetrogeneDB ID: retro_pabe_611

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:85011760..85012592(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSU1
• Ensembl ID: ENSPPYG00000002120
• Aliases: None
• Description: ras suppressor protein 1 [Source:RefSeq peptide;Acc:NP_001126192]

Sequence

>retro_pabe_611
TTAGGTGCTGCTCTTCGCGACCATGTCCAAGACTCTGAAAAAGTTTGTGGAGCGCCAGGAAGTGGACAGGGTGACTAGGT
CATCTACAACATGCTGTATGTCAATGGCACATTTTCCTTATCCCATACCATACGACTGGTCCTCAGCCATAACAAGCTCA
CAGTGGTGCCACCAAACACAGCAGAACTGAAGAATTTGGAAGTGCTCAACTTCCTTAATAGCCAGATTGAGGAGCTGCCC
ACACAGATCAGCAGCCTTCAGAAACTCTAACACGTGAATGTGGGCATGAATGGGCTAAATACTTTGCCTGAAGGATTTTG
CCTTCTACCCAGCTCTTGACCTTCTGGACTTGATGTACAATTTGAGTGAAAATTCTCTTCCTGGAAACTTCATGTACCTT
ACCACTTTCCGTGCACTCATATGTAAGTGACAATGATTTTGAAATCCTGCAACCAGATATTAGGAAGCTCACAAAGTTGC
AGATACCCAGCTTTAGGGATAACAACCTGATCTTGCAGCCTAGGGAAACTGGGGAGCTTACCCAGCTTAAGAAACTCAAC
ATTCAGGGCAACTGCCTGACCCTTCTGCTCTCAGAACTAGGAAACTTATATTTAACTGGTCAGAAGAAGGTATACAAAGT
GGAGAACAACCCCTGGGTTACCCCAATTGCTGGCCAGTTCCAGCTTGATGTGTCCTGTGTGTTTGAATGTGTCTGTTCTG
AGACATGTGAGTACCTCTATGGCAGCACATGCAGGCAAATCCAGAACCACCAAAAAATAATAATCACAAATCAGAAAAGA
TGAGCTGGAAACACCTGACAGCCGGTAACAAA

Alignment

ORF - retro_pabe_611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.04 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSKSLKKLVEESREK-NQPEVDMSDRGISNMLDVNGLFTLSHITQLVLSHNKLTTVPPNIAELKNLEVLN
          ....L...V..S......P.....D..I.NML.VNG.F.LSH...LVLSHNKLT.VPPN.AELKNLEVLN
Retrocopy LGAALRDHVQDSEKVCGAPGSGQGD*VIYNMLYVNGTFSLSHTIRLVLSHNKLTVVPPNTAELKNLEVLN

Parental  FFNNQIEELPTQISSLQKLKHLNLGMNRLNTLPRGFGSLP-ALEVLDLTYNNLSENSLPGNFFYLTTLRA
          F.N.QIEELPTQISSLQKL.H.N.GMN.LNTLP.GF..LP.AL..LDL.YN.LSENSLPGNF.YLTT.RA
Retrocopy FLNSQIEELPTQISSLQKL*HVNVGMNGLNTLPEGFCLLP>ALDLLDLMYN-LSENSLPGNFMYLTTFRA

Parental  L-YLSDNDFEILPPDIGKLTKLQILSLRDNDLISLPKEIGELTQLKELHIQGNRLTVLPPELGNLDLTGQ
          L.Y.SDNDFEIL.PDI.KLTKLQI.S.RDN.LI..P.E.GELTQLK.L.IQGN.LT.L..ELGNL.LTGQ
Retrocopy L>YVSDNDFEILQPDIRKLTKLQIPSFRDNNLILQPRETGELTQLKKLNIQGNCLTLLLSELGNLYLTGQ

Parental  KQVFKAENNPWVTPIADQFQLGVSHVFEYIRSETYKYLYG-RHMQANPEPPKKNNDKSKKISRKPLAAKN
          K.V.K.ENNPWVTPIA.QFQL.VS.VFE...SET..YLYG..HMQANPEPPK.NN.KS.K.S.K.L.A.N
Retrocopy KKVYKVENNPWVTPIAGQFQLDVSCVFECVCSETCEYLYG<QHMQANPEPPKNNNHKSEKMSWKHLTAGN

Parental  R
          .
Retrocopy K

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	14.82 RPM
SRP007412_cerebellum	0.00 RPM	12.04 RPM
SRP007412_heart	0.21 RPM	15.38 RPM
SRP007412_kidney	0.03 RPM	17.63 RPM
SRP007412_liver	0.06 RPM	15.88 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_611 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_611 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_611 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_575
Pan troglodytes	retro_ptro_425
Gorilla gorilla	retro_ggor_512

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000148484	1 retrocopy	retro_hsap_575,
Gorilla gorilla	ENSGGOG00000028048	1 retrocopy	retro_ggor_512,
Macropus eugenii	ENSMEUG00000006702	1 retrocopy	retro_meug_2092,
Macaca mulatta	ENSMMUG00000016067	1 retrocopy	retro_mmul_712,
Monodelphis domestica	ENSMODG00000009942	1 retrocopy	retro_mdom_338,
Nomascus leucogenys	ENSNLEG00000012444	1 retrocopy	retro_nleu_462,
Pongo abelii	ENSPPYG00000002120	1 retrocopy	retro_pabe_611 ,
Pan troglodytes	ENSPTRG00000002325	1 retrocopy	retro_ptro_425,
Tarsius syrichta	ENSTSYG00000002386	1 retrocopy	retro_tsyr_730,