RetrogeneDB ID: retro_pabe_3581

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:24614529..24615805(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK25
• Ensembl ID: ENSPPYG00000025879
• Aliases: None
• Description: serine/threonine kinase 25 [Source:HGNC Symbol;Acc:11404]

Sequence

>retro_pabe_3581
ATGGCTCACTTCCGGGGACTTGCCAACGAGCACTCTCGCGTGGACCCTGAAGAGCTCTTCACCAAGCTCGACCGCACGGG
CAAGGGCTCGTTCGGGGAAGTCTACAAGGGCATCGATAACCACACGAAGGAGGTGGTGGCCCTCAAGATCATCGACCTGG
AGGAGGCCGAGGAGGAGACCGAGGACATCCAGCAGGAGATCACCGTCCTCAGCCAGTGCGACAGCCCCTAAGTCACCCGC
TACTTTGGCTCCTACCTAAAGAGCACCAAGCTATGGATCATCATGGAGTACCTGGGCGGCGGCTCAGCACTGGACTTGCT
TAAACCAGGTCCCCTGGAGGAGACGTACATTGCCACGATCCTGCGGGAGATTCTGAAGGGCCTGGATTATCTGCACTCCC
AATGCAAGATCCACCGATACATCAAAGCTGCCAACGTGCCACTCTCGGAGCAGGGGGACGTGAAGCTGGCGGACTTTGGG
GTAGCAGGGCAGCTCACAGACACGCAGATTAAGAGGAACACATTCGTGGGCACCCCCTTCTGGATGGCGCCTGAGGTCAT
CAAGCAGTCGGCCTACGACTTTAAGGCTGACATCTGGTCCCTGGGGATCACGGCCATCGAGCTGGCCAAGGGGGAGCCTC
CATCTCTGACCTCCACCCCATGTGCGTCCTGTTCCTGATTCCCAAGAACAGCCCACCCACGCTGGAGGGCCAGCACAGCA
AGCCCTTCAAGGAGTTCATGGGGGCCTCCCTCAACAAGGACGCCCGATTCCGGCCCACCGCCAAGGAGCTCCTGAAGCAA
ATTCATCACACGCTACATCACGAAGACCTCCTTCCTCACCGAGCTCATTGAGCGCTATAAGCGCTGGAAGTCAGAGGGGC
ATGGTGAGGAGTCCAGCTCTGAGGACTCTGACATTGATGGCGAGGGGGAGGACCGGGAGCAGGGCCCCATCTGGACGTTC
CCCCCCCACCATCCGGCGGAGTCCACACAGCAAGCTTCACAAGTGGACAGCCCTGCATGGCTCACAGAAGCCTGTGGAGC
CCGTCAAGAGGCAGCCAAGGTCCCAGTGCCTGTCCACGCTGGTCCGGCCCGTCTTCGGAGAGCTCAAAGAGAAGCACGAG
CAGAGCGGCGGGAGCGTGGGTGCGCTGGAGGAGCTGGAGAACGCCTTCAGACAGGCGGAGGAGTCCTGCCCCGGCATCTC
AGACAAGCTGATGGTGCACCTGGTGGAGCGAGTGCAGAGGTTTTCACACAACAGAAACCACCTGACATCCACCCGC

Alignment

ORF - retro_pabe_3581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAHLRGFANQHSRVDPEELFTKLDRIGKGSFGEVYKGIDNHTKEVVAIKIIDLEEAEDEIEDIQQEITVL
          MAH.RG.AN.HSRVDPEELFTKLDR.GKGSFGEVYKGIDNHTKEVVA.KIIDLEEAE.E.EDIQQEITVL
Retrocopy MAHFRGLANEHSRVDPEELFTKLDRTGKGSFGEVYKGIDNHTKEVVALKIIDLEEAEEETEDIQQEITVL

Parental  SQCDSPYITRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHRD
          SQCDSP..TRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHS..KIHR.
Retrocopy SQCDSP*VTRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSQCKIHRY

Parental  IKAANVLLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIELAK
          IKAANV.LSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIELAK
Retrocopy IKAANVPLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIELAK

Parental  GEPPN-SDLHPMRVLFLIPKNSPPTLEGQHSKPFKEFVEACLNKDPRFRPTAKELLKHKFITRY-TKKTS
          GEPP..SDLHPM.VLFLIPKNSPPTLEGQHSKPFKEF..A.LNKD.RFRPTAKELLK....T...TK.TS
Retrocopy GEPPS<SDLHPMCVLFLIPKNSPPTLEGQHSKPFKEFMGASLNKDARFRPTAKELLKQIHHTLH>TK-TS

Parental  FLTELIDRYKRWKSEGHGEESSSEDSDIDGEAEDGEQGPIWT-FPPTIRPSPHSKLHKGTALHGSQKPAE
          FLTELI.RYKRWKSEGHGEESSSEDSDIDGE.ED.EQGPIWT....TIR.SPHSKLHK.TALHGSQKP.E
Retrocopy FLTELIERYKRWKSEGHGEESSSEDSDIDGEGEDREQGPIWT>XXXTIRRSPHSKLHKWTALHGSQKPVE

Parental  PVKRQPRSQCLSTLVRPVFGELKEKHKQSGGSVGALEELENAFSLAEESCPGISDKLMVHLVERVQRFSH
          PVKRQPRSQCLSTLVRPVFGELKEKH.QSGGSVGALEELENAF..AEESCPGISDKLMVHLVERVQRFSH
Retrocopy PVKRQPRSQCLSTLVRPVFGELKEKHEQSGGSVGALEELENAFRQAEESCPGISDKLMVHLVERVQRFSH

Parental  NRNHLTSTR
          NRNHLTSTR
Retrocopy NRNHLTSTR

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	80.17 RPM
SRP007412_cerebellum	0.00 RPM	72.47 RPM
SRP007412_heart	0.00 RPM	26.61 RPM
SRP007412_kidney	0.00 RPM	64.37 RPM
SRP007412_liver	0.00 RPM	34.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3581 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3581 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3581 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006066	1 retrocopy	retro_cjac_1090,
Gorilla gorilla	ENSGGOG00000004267	1 retrocopy	retro_ggor_956,
Pongo abelii	ENSPPYG00000025879	5 retrocopies	retro_pabe_1082, retro_pabe_1697, retro_pabe_3581 , retro_pabe_3584, retro_pabe_683,