RetrogeneDB ID: retro_pabe_1082

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13_random:9873128..9874395(+)
• 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_1082
ATGGCTCACCTCCGGGGATTTGCCAACCAGCACTCTGGAGTGGACCCTGAAGAGCTCTTCACCAAGCTCGACTGCATTGG
CAAGGGCTCGTTTGGGTAGGTCTACAAGGGCATGGATAACCACACGAAGGAGGTGGTGGCCATCAAGATCGTCCACCTGG
AGGAGGCCGAGGATGAGATCGAGGACATGCAGCAGGAGATCACCGTCCTCAGCCAGTGCGACAGCCCCTACATCACCCGC
TACTTTGGCTCCTACCTAAAGAGCACCAAGCTATGGATCATCATGGAGTACCTGGGCGGCGGCTCAGCACTGGATTTGCT
TAAACCAGGTCCCCTGGAGGAGACGTACATTGCCACGATCCTGCGGGAGATTCTGAAGGGCCTGGATTATCTGCACTCCG
AACGCAAGATCCACCCAGACATCAAAGCTGCCAACGTGCTACTCTTGGAGCAGGGGGACGTGAAGCTGGTGGACTTTGGG
GTAGCAGGGCACCTCACAGACATGCAGATTAAGAGGAACACATTCGTGGGCACCCCCTTCTGGATGGCGCCTGAGGTCAT
CAAGCAGTCGGCCTACGACTTCAAGGCTGACATCTGGTCCCTGGGGATCACGGCCATCGAGCTGGCCAAGGGGGAGCCTC
CAAACTCTGACCTCCACCCCATGCGCGTCCTGTTCCTGATTCCCAAGAACAGCCCACCCACACTGGAGGGCCAGCACAGC
AAGCCCTTCAAGGAGTTCCTGGAGGCCTGCCTCAACAAGGACCTCCCAATTCCGGCCCACGGCCAAGGAGCTCCTGAAGC
ACAAATTCATGACACGCTACACCAAGAAGACTTCCTTCCTCACCGAGTTCATCCACCGCTATAAGCGCTGGAAGTCAGAG
GGGCATGGCGAGGAGTCCAGCTCTGAGGACTCTGACATTGATGGCGAGATGGAGGACGAGGAGCAGGGCCCCATCTGGAC
GTTCCCCCCTACCATCCGGCCGAGTCCACACAGCAAGCTTCACAAGGGGACGGCCCTGCATGGCTCACAGAAGCCTGCGG
AGCCCGTCAAGAGGCAGCCGAGGTTCCAGTGCCTGTCCACGCTGGTCCGGCCCGTCTTCGGAGAGCTCAAAGAGAAGCAC
AAGCAGAGCGGCGGAAGCCTGGGTGAGCTGGAGGAGCTGGAGAAGGCCTTCAGCCTGGCCGAGGAGTCCTGCCCTGGCAT
CTCAGACAAGCTGACGATGCACCTGGTGGAGCGAGTGCAGAGGTTTTCACACAACAGAAACCTGCTG

Alignment

ORF - retro_pabe_1082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.38 %
• Parental protein coverage: 99.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAHLRGFANQHSRVDPEELFTKLDRIGKGSFGEVYKGIDNHTKEVVAIKIIDLEEAEDEIEDIQQEITVL
          MAHLRGFANQHS.VDPEELFTKLD.IGKGSFG.VYKG.DNHTKEVVAIKI..LEEAEDEIED.QQEITVL
Retrocopy MAHLRGFANQHSGVDPEELFTKLDCIGKGSFG*VYKGMDNHTKEVVAIKIVHLEEAEDEIEDMQQEITVL

Parental  SQCDSPYITRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHRD
          SQCDSPYITRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIH.D
Retrocopy SQCDSPYITRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHPD

Parental  IKAANVLLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIELAK
          IKAANVLL.EQGDVKL.DFGVAG.LTD.QIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIELAK
Retrocopy IKAANVLLLEQGDVKLVDFGVAGHLTDMQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIELAK

Parental  GEPPNSDLHPMRVLFLIPKNSPPTLEGQHSKPFKEFVEACLNKD-PRFRPTAKELLKHKFITRYTKKTSF
          GEPPNSDLHPMRVLFLIPKNSPPTLEGQHSKPFKEF.EACLNKD...FRPTAKELLKHKF.TRYTKKTSF
Retrocopy GEPPNSDLHPMRVLFLIPKNSPPTLEGQHSKPFKEFLEACLNKD>SQFRPTAKELLKHKFMTRYTKKTSF

Parental  LTELIDRYKRWKSEGHGEESSSEDSDIDGEAEDGEQGPIWTFPPTIRPSPHSKLHKGTALHGSQKPAEPV
          LTE.I.RYKRWKSEGHGEESSSEDSDIDGE.ED.EQGPIWTFPPTIRPSPHSKLHKGTALHGSQKPAEPV
Retrocopy LTEFIHRYKRWKSEGHGEESSSEDSDIDGEMEDEEQGPIWTFPPTIRPSPHSKLHKGTALHGSQKPAEPV

Parental  KRQPRSQCLSTLVRPVFGELKEKHKQSGGSVGALEELENAFSLAEESCPGISDKLMVHLVERVQRFSHNR
          KRQPR.QCLSTLVRPVFGELKEKHKQSGGS.G.LEELE.AFSLAEESCPGISDKL..HLVERVQRFSHNR
Retrocopy KRQPRFQCLSTLVRPVFGELKEKHKQSGGSLGELEELEKAFSLAEESCPGISDKLTMHLVERVQRFSHNR

Parental  NHL
          N.L
Retrocopy NLL

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_1082 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1082 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1082 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,