RetrogeneDB ID: retro_pabe_3584

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:28357504..28358301(-)
• 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_3584
ATGGCTCACCTCCGGGGACTTGCCAACGAGCACTCTCGAGTGGACCCTGAAGTGCTCTTCACCAAGCTCGACCGCACGGG
CAAGGGCTCGTTCGGGGAAGTCTACAAGGGCATCGATAACCACACGAAGGAGGTGGTGGCCCTCAAGATCATCGACCTGG
AGGAGGCCGAGGAGGAGACCGAGGACATCCAGCAGGAGATCACCGTCCTCAGCCAGTGCGACAGCCCCTACGTCACCCGC
TACTTTGGCTCCTACCTAAAGAGCACCAAGCTATGGATCATCATGGAGTACCTGGGCGGCGGCTCAGCACTGGACTTGCT
TAAACCAGGTCCCCTGGAGGAGACGTACATTGCCACGATCCTGCGGGAGATTCTGAAGGGCCTGGATTATCTGCACTCCG
AACGCAAGATCCACCCAGACATCAAAGCTGCCAACGTGCCACTCTCGGAGCAGGGGGACGTGAAGCTGGCGGACTTTGGG
GTAGCAGGGCAGCTCACAGACACGCAGATTAAGAGGAACACATTCGTGGGCACCCCCTTCTGGATGGCGCCTGAGATCAT
CAAGCAGTCGGCCTACGACTTTAAGGCTGACATCTGGTCCCTGGGGATCACGGCCATCGAGCTGGCCAAGGGGGAGCCTC
CATCTCTGACCTCCACCCCATGTGCGTCCTGTTCCTGATTCCCAAGAACAGCCCACCCACGCTGGAGGGCCAGCACAGCA
AGCCCTTCAAGGAGTTCATGGGGGCCTCCCTCAACAAGGACGCCCGATTCCGGCCCACCGCCAAGGAGCTCCTGAAG

Alignment

ORF - retro_pabe_3584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.26 %
• Parental protein coverage: 62.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAHLRGFANQHSRVDPEELFTKLDRIGKGSFGEVYKGIDNHTKEVVAIKIIDLEEAEDEIEDIQQEITVL
          MAHLRG.AN.HSRVDPE.LFTKLDR.GKGSFGEVYKGIDNHTKEVVA.KIIDLEEAE.E.EDIQQEITVL
Retrocopy MAHLRGLANEHSRVDPEVLFTKLDRTGKGSFGEVYKGIDNHTKEVVALKIIDLEEAEEETEDIQQEITVL

Parental  SQCDSPYITRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHRD
          SQCDSPY.TRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIH.D
Retrocopy SQCDSPYVTRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHPD

Parental  IKAANVLLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIELAK
          IKAANV.LSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPE.IKQSAYDFKADIWSLGITAIELAK
Retrocopy IKAANVPLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEIIKQSAYDFKADIWSLGITAIELAK

Parental  GEPPN-SDLHPMRVLFLIPKNSPPTLEGQHSKPFKEFVEACLNKDPRFRPTAKELLK
          GEPP..SDLHPM.VLFLIPKNSPPTLEGQHSKPFKEF..A.LNKD.RFRPTAKELLK
Retrocopy GEPPS<SDLHPMCVLFLIPKNSPPTLEGQHSKPFKEFMGASLNKDARFRPTAKELLK

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	0.06 RPM	80.17 RPM
SRP007412_cerebellum	0.00 RPM	72.47 RPM
SRP007412_heart	0.00 RPM	26.61 RPM
SRP007412_kidney	0.03 RPM	64.37 RPM
SRP007412_liver	0.03 RPM	34.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3584 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3584 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3584 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,