RetrogeneDB ID: retro_pabe_1697

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19_random:7238902..7240177(+)
• 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_1697
ATGGCTCACCTTCGGGGACTTGCCAACGAGCACTCTCGAGTGGACCCTGAAGAGCTCTTCATCAAGCTCGACCGCACGGG
CAAGGGCTCGTTCGGGGAAGTCTACAAGGGCATCGATAACCACACGAAGGAGGTGGTGGCCCTCAAGATCATCGACCTGG
AGGAGGCCGAGGAGGAGACCGAGGACATCCAGCAGGAGATCACCGTCCTCAGCCAGTGCGACAGCCCCTACGTCACCCAC
TACTTTGGCTCCTACCTAAAGAGCACCAAGCTATGGATCATCATGGAGTACCTGGGCGGCGGCTCAGCACTGGACTTGCT
TAAACCAGGTCCCCTGGAGGAGACGTACATTGCCACGATCCTGCGGGAGATTCTGAAGGGCCTGGATTATCTGCACTCCC
AATGCAAGATCCACCGATACATCAAAGCTGCCAACGTGCCACTCTCGGAGCAGGGGGACGTGAAGCTGGCGGACTTTGGG
GTAGCAGGGCAGCTCACAGACACGCAGATTAAGAGGAACACATTCGTGGGCACCCCCTTCTGGATGGCGCCTGAGGTCAT
CAAGCAGTCGGCCTACGACTTTAAGGCTGACATCTGGTCCCTGGGGATCACGGCCATCCAGCTGGCCAAGGGGGAGCCTC
CATCTCTGACCTCCACCCCATGCGCGTCCTGTTCCTGATTCCCAAGAACAGCCCACCCACGCTGGAGGGCCAGCACAGCA
AGCCTTTCAAGGAGTTCATGGGGGCCTCTCTCAACAAGGACGCCCGATTCCGGCCCACCGCCAAGGAGCTCCTGAAGCAA
ATTCATCACACGCTACATCACGAAGACCTCCTTCCTCACCGAGCTCATTGAGCGCTATAAGCGCTGGAAGTCAGAGGGGC
ATGGTGAGGAGTCCAGCTCTGAGGACTCTGACATTGATGGCGAGGGGGAGGACCGGGAGCAGGGCCCCATCTGGACGTTC
CCCCCCACCATCCGGCGGAGTCCACACAGCAAGCTTCACAAGTGGACAGCCCTGCATGGCTCACAGAAGCCTGTGGAGCC
CGTCAAGAGGCAGCCAAGGTCCCAGTGCCTGTCCACGCTGGTCCGGCCCGTCTTCGGAGAGCTCAAAGAGAAGCACAAGC
AGAGCGGCGGGAGCGTGGGTGCGCTGGAGGAGCTGGAGAACGCCTTCAGACAGGCGGAGGAGTCCTGCCCCGGCATCTCA
GACAAGCTCATGGTGCACCTGGTGGAGCGAGTGCAGAGGTTTTCACACAACAGAAACCACCTGACATCCACCCGC

Alignment

ORF - retro_pabe_1697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAHLRGFANQHSRVDPEELFTKLDRIGKGSFGEVYKGIDNHTKEVVAIKIIDLEEAEDEIEDIQQEITVL
          MAHLRG.AN.HSRVDPEELF.KLDR.GKGSFGEVYKGIDNHTKEVVA.KIIDLEEAE.E.EDIQQEITVL
Retrocopy MAHLRGLANEHSRVDPEELFIKLDRTGKGSFGEVYKGIDNHTKEVVALKIIDLEEAEEETEDIQQEITVL

Parental  SQCDSPYITRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHRD
          SQCDSPY.T.YFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHS..KIHR.
Retrocopy SQCDSPYVTHYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSQCKIHRY

Parental  IKAANVLLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIELAK
          IKAANV.LSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAI.LAK
Retrocopy IKAANVPLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIQLAK

Parental  GEPPN-SDLHPMRVLFLIPKNSPPTLEGQHSKPFKEFVEACLNKDPRFRPTAKELLKHKFITRY-TKKTS
          GEPP..SDLHPMRVLFLIPKNSPPTLEGQHSKPFKEF..A.LNKD.RFRPTAKELLK....T...TK.TS
Retrocopy GEPPS<SDLHPMRVLFLIPKNSPPTLEGQHSKPFKEFMGASLNKDARFRPTAKELLKQIHHTLH>TK-TS

Parental  FLTELIDRYKRWKSEGHGEESSSEDSDIDGEAEDGEQGPIWTFPPTIRPSPHSKLHKGTALHGSQKPAEP
          FLTELI.RYKRWKSEGHGEESSSEDSDIDGE.ED.EQGPIWTFPPTIR.SPHSKLHK.TALHGSQKP.EP
Retrocopy FLTELIERYKRWKSEGHGEESSSEDSDIDGEGEDREQGPIWTFPPTIRRSPHSKLHKWTALHGSQKPVEP

Parental  VKRQPRSQCLSTLVRPVFGELKEKHKQSGGSVGALEELENAFSLAEESCPGISDKLMVHLVERVQRFSHN
          VKRQPRSQCLSTLVRPVFGELKEKHKQSGGSVGALEELENAF..AEESCPGISDKLMVHLVERVQRFSHN
Retrocopy VKRQPRSQCLSTLVRPVFGELKEKHKQSGGSVGALEELENAFRQAEESCPGISDKLMVHLVERVQRFSHN

Parental  RNHLTSTR
          RNHLTSTR
Retrocopy RNHLTSTR

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_1697 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1697 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1697 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,