RetrogeneDB ID: retro_pabe_125

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:48585670..48587149(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020301
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: WASF2
• Ensembl ID: ENSPPYG00000001661
• Aliases: None
• Description: WAS protein family, member 2 [Source:HGNC Symbol;Acc:12733]

Sequence

>retro_pabe_125
AACGAGAACATCGAGCCAAGGCACCTGTGCCGTCAGAGGTTGCCTAGCGTTAGAAGCAAGCTGGAATGCGTGACCAACAT
CACCCTGGCAAATGTCATCCGACAGCTGGGCAGCCTGAGTAAATATGCAGAGGACATTTTTGGAGAGCTCTTTACTCAGG
CAAATACCTTTGCCTCTCGGGTAAGCTCCCTTGCTGAGAGGGTCAACGGACTACAAGTTAAAGTCACTCAGCTGGATCCC
AAGGAAGAAGAAGGGTCACTGCAAGGAATCAACCCCCGAAAAGCCTTCAGAAGCTCCATCATTCAAGACCAGAAGCTTTT
TGACAGAAACTCTCTCCCAGTGCCTGTCTTAGAAACATACAAGACCTGTGATACTCCTCCCCCTCTCAACAATCTTACCC
CTTACAGGGAAGATGGAAAAGAGGCACTCAAATTCTACACAGACCCTTCATACTTCTTTGATCTTTGGAAGGAGAAGATG
CTGCAGGACACCAAGGATATCATGAAAGAGAAGAGAAAGCATAGGAAAGAAAAGAAAGATAATCCAAATCGAGGGGATGT
AAACCCATGTAAAATCAAGACACGTAAGGAAGAGTGGGAGAAAATTAAGATGGGGCAAGAATTTGTGGAGTCCAAAGAAA
AGGTGGGGCCTTCTGGGTATCCACCCACCTTGGTGTACCAGAATGGCAGCATTGGCTGTGTTGAAAACATGGATGCAAGT
AGCTATCCACCACCATCACAGTCAGACTCTGCTTCTTCACCTTCTCCTTCCTTCGAGGACAACTTGCCTCCTCCACCAGC
AGAATTCAGTTACCCAGTGGACAACCAAAGAGGGTCTGGTTTGGCTGGACCCAAAAGATCCAGTGTGGTCAGCCCAAGCC
ATCCACCACCAGTTCCTCCTCTAGGCTCTCCACCAGGCCCTAAACCCGGGTTTGCTCCACCACCTGCCCCTCCACCACCT
CCACCTCCAATGATAGGCATCCCACCTCCACCACTGCCTGTAGGATTTGGGTCTCCAGGGACGCCTCCACCACCCTCACC
CCCATCTTTCCCACCTCACCCTGATTTTGCTGCCCCTCCACCTCCTCCTCTACCACCGGCAGCTGACTACCCAACTCTGC
CACCACCTCCCTTGTCCCAGCCAACAGGAGGATCACCTCCTTCTCCCCCTCCTCCTCCTCCTCCGGGGCCCCCTCCTCCC
CCTTTCACTGGTGCAGATGGCCAGCCTGCTCTACCACCACCGCTTTCTGATACCACCAAGTCCAAGTCCTCCTTGCCTGC
CGTAAGCGATGCCCGTAGCGACCTGCTTTCAGCCATCCGTCAAGGTTTTCAGCTGCGCAGGGTTGAGGAGCAGCAGGAAC
AAGAGAAGCGGGATGTCGTGGGCAATGACGTGGCCACCGTCGTGTCTCGTCTCATTGCTGTTGAGTACAGTGACTCAGAA
GATGACTCCTCTGAATTTGATGAGGACGACTGGTCCGAT

Alignment

ORF - retro_pabe_125 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.66 %
• Parental protein coverage: 82.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NIEPRHLCRQTLPSVRSELECVTNITLANVIRQLGSLSKYAEDIFGELFTQANTFASRVSSLAERVDRLQ
          NIEPRHLCRQ.LPSVRS.LECVTNITLANVIRQLGSLSKYAEDIFGELFTQANTFASRVSSLAERV..LQ
Retrocopy NIEPRHLCRQRLPSVRSKLECVTNITLANVIRQLGSLSKYAEDIFGELFTQANTFASRVSSLAERVNGLQ

Parental  VKVTQLDPKEEEVSLQGINTRKAFRSSTIQDQKLFDRNSLPVPVLETYNTCDTPPPLNNLTPYRDDGKEA
          VKVTQLDPKEEE.SLQGIN.RKAFRSS.IQDQKLFDRNSLPVPVLETY.TCDTPPPLNNLTPYR.DGKEA
Retrocopy VKVTQLDPKEEEGSLQGINPRKAFRSSIIQDQKLFDRNSLPVPVLETYKTCDTPPPLNNLTPYREDGKEA

Parental  LKFYTDPSYFFDLWKEKMLQDTKDIMKEKRKHRKEKKDNPNRGNVNPRKIKTRKEEWEKMKMGQEFVESK
          LKFYTDPSYFFDLWKEKMLQDTKDIMKEKRKHRKEKKDNPNRG.VNP.KIKTRKEEWEK.KMGQEFVESK
Retrocopy LKFYTDPSYFFDLWKEKMLQDTKDIMKEKRKHRKEKKDNPNRGDVNPCKIKTRKEEWEKIKMGQEFVESK

Parental  EKLGTSGYPPTLVYQNGSIGCVENVDASSYPPPPQSDSASSPSPSFSEDNLPPPPAEF
          EK.G.SGYPPTLVYQNGSIGCVEN.DASSYPPP.QSDSASSPSPSF.EDNLPPPPAEF
Retrocopy EKVGPSGYPPTLVYQNGSIGCVENMDASSYPPPSQSDSASSPSPSF-EDNLPPPPAEF

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	1.11 RPM	7.80 RPM
SRP007412_cerebellum	0.73 RPM	7.54 RPM
SRP007412_heart	8.07 RPM	5.15 RPM
SRP007412_kidney	3.18 RPM	14.78 RPM
SRP007412_liver	1.32 RPM	4.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_125 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_125 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_125 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4682
Gorilla gorilla	retro_ggor_2904

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000158195	1 retrocopy	retro_hsap_4682,
Gorilla gorilla	ENSGGOG00000004436	1 retrocopy	retro_ggor_2904,
Nomascus leucogenys	ENSNLEG00000009635	1 retrocopy	retro_nleu_2175,
Pongo abelii	ENSPPYG00000001661	1 retrocopy	retro_pabe_125 ,