RetrogeneDB ID: retro_pabe_683

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:24629449..24630723(+)
• Located in intron of: ENSPPYG00000003338

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_683
ATGGCTCACCTCCGGGGATTTGCCAACCAGCACTCTCGAGTGGACCCTGAAGAGCTCTTCACCAAGCTCGACCGCATTGG
CAAGGGCTCCTTTGGTGAGGTCTACAAGGGCATCGATAACCACACGAAGGAGGTGGTGGCCCTCAAGATCATCGACCTGG
AGGAGGCCGAGGATGAGATCGAGGACATCCAGCAGGAGATCACCGTCCTCAGCCAGTGCGACAGCCCCTACATCACCCGC
TACTTTGGCTCCTACCTAAAGAGCACCAAGTATGGATCATCATGGAATACCTGGGTGGCGGCTCAGCACTGGACTTGCTT
AAACCAGGTCCCCTGGAGGAGACGTACATTGCCACGATCCTGCGGGAGATTCTGAAGGGCCTGGATTATCTGCACTCCGA
ACGCAAGATCCACCCAGACATCAAAGCTGCCAACGTGCTACTCTCGGAGCAGGGGGACGTGAAGCTGGCGGACTTTGGGG
TAGCAGGGCAGCTCACAGACACGCAGATTAAGAGGAACACATTCGTGGGCACCCCCTTCTGGATGGCGCCTGAGGTCATC
AAGCAGTCGGCCTACAACTTCAAGGCTGACATCTGGTCCCTGGGGATCACGGCCATCGAGCTGGCCAAGGGGGAGCCTCC
AAACTCTGACCTCCACCCCATGTGCGTCCTGTTCCTGATTCCCAAGAACAGCCCACCCACACTGGAGGGCCAGCACAGCA
AGCCCTTCAAGGAGGTCGTGGAGGCCTGCCTCAACAAAGACCCCCGATTTCGGCCCACGGCCAAGGAGCTCCTGAAGCAC
AAGTTCATCACATGCTACACCAAGAAGACCTCCTTCCTCACGGAGCTCATCGACCGCTATAAGCGCTGGAAGTCAGAGGG
GCATGGCGAGGAGTCCAGCTCTGAGGACTCTGACATTGATGGCGAGGCGGAGGACGGGGAGCAGGGCCCCATCTGGACGT
TCCCCCCTACCATCCGGCCGAGTCCACACAGCAAGCTTCACAAGGGGACGGCCCTGCACAGCTCATAGAAGCCTGTGGAG
CCCGTCAAGAGGCAGCTGAGGTCCCAGTGCCTGTCCACGCTGGTCCGGCCCGTCTTGGGAGAGCTCAAAGAGAAGCACAA
GCAGAGCGGCAGGAGTGTGGGTGCGCTGGAGGAGCTGGAGAATGCCTTCAGCCTGGCTGAGGAGTCCTGCCCCGGCATCT
CAGACAAGCTGATGGTGCACCTGGTGGAGCGAGTGCAGAGGTTTTCACACAACAGAAACCACCTGACATCCACC

Alignment

ORF - retro_pabe_683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.71 %
• Parental protein coverage: 99.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAHLRGFANQHSRVDPEELFTKLDRIGKGSFGEVYKGIDNHTKEVVAIKIIDLEEAEDEIEDIQQEITVL
          MAHLRGFANQHSRVDPEELFTKLDRIGKGSFGEVYKGIDNHTKEVVA.KIIDLEEAEDEIEDIQQEITVL
Retrocopy MAHLRGFANQHSRVDPEELFTKLDRIGKGSFGEVYKGIDNHTKEVVALKIIDLEEAEDEIEDIQQEITVL

Parental  SQCDSPYITRYFGSYLKSTK-LWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHR
          SQCDSPYITRYFGSYLKSTK..WIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIH.
Retrocopy SQCDSPYITRYFGSYLKSTK<VWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHP

Parental  DIKAANVLLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIELA
          DIKAANVLLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAY.FKADIWSLGITAIELA
Retrocopy DIKAANVLLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYNFKADIWSLGITAIELA

Parental  KGEPPNSDLHPMRVLFLIPKNSPPTLEGQHSKPFKEFVEACLNKDPRFRPTAKELLKHKFITRYTKKTSF
          KGEPPNSDLHPM.VLFLIPKNSPPTLEGQHSKPFKE.VEACLNKDPRFRPTAKELLKHKFIT.YTKKTSF
Retrocopy KGEPPNSDLHPMCVLFLIPKNSPPTLEGQHSKPFKEVVEACLNKDPRFRPTAKELLKHKFITCYTKKTSF

Parental  LTELIDRYKRWKSEGHGEESSSEDSDIDGEAEDGEQGPIWTFPPTIRPSPHSKLHKGTALHGSQKPAEPV
          LTELIDRYKRWKSEGHGEESSSEDSDIDGEAEDGEQGPIWTFPPTIRPSPHSKLHKGTALH.S.KP.EPV
Retrocopy LTELIDRYKRWKSEGHGEESSSEDSDIDGEAEDGEQGPIWTFPPTIRPSPHSKLHKGTALHSS*KPVEPV

Parental  KRQPRSQCLSTLVRPVFGELKEKHKQSGGSVGALEELENAFSLAEESCPGISDKLMVHLVERVQRFSHNR
          KRQ.RSQCLSTLVRPV.GELKEKHKQSG.SVGALEELENAFSLAEESCPGISDKLMVHLVERVQRFSHNR
Retrocopy KRQLRSQCLSTLVRPVLGELKEKHKQSGRSVGALEELENAFSLAEESCPGISDKLMVHLVERVQRFSHNR

Parental  NHLTST
          NHLTST
Retrocopy NHLTST

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	0.50 RPM	80.17 RPM
SRP007412_cerebellum	0.12 RPM	72.47 RPM
SRP007412_heart	0.06 RPM	26.61 RPM
SRP007412_kidney	0.10 RPM	64.37 RPM
SRP007412_liver	0.09 RPM	34.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_683 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_683 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 ,