RetrogeneDB ID: retro_pabe_2020

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a_random:1981894..1983114(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLF4
• Ensembl ID: ENSPPYG00000019478
• Aliases: None
• Description: Kruppel-like factor 4 (gut) [Source:HGNC Symbol;Acc:6348]

Sequence

>retro_pabe_2020
ATGAGGCAGCCACCTGGCGAGTCTGACATGGCTGTCAGCGACGCGCTGCTCCCATCTTTCTCCACGTTCGCGTCTGGCCC
GGCGGGAAGGGAGAAGACACTGCGTCAAGCAGGTGCCCCGAATAACCGCTGGCGGGAGGAGCTCTCCCACATGAAGCGAC
TTCCCCCGGTGCTTCCCGGCCGCCCCTATGACCTGGCGGCGGCGACCGTGGCCACAGACCTGGAGAGCGGCGGAGCCGGT
GCCGCTTGCGGCGGTAGCAACCTGGCGCCCCTACCTCGGAGAGAGACCGAGGAGTTCAACGATCTCCTGGACCTGGACTT
TATCCTCTCTAATTCGCTGACCCATCCTCCGGAGTCAGTGGCCGCCACCGTGTCCTCGTCAGCGTCAGCCTCCTCCTCGT
CGTCCCCGTCGAGCAGCGGCCCTGCCAGCGCGCCCTCCACCTGCAGCTTCACCTATCCGATCCGGGCCGGGAACGACCCG
GGCGTGGCGCCGGGCGGCACGGGCGGAGACCTCTTGATGGCAGGGAGTCCGCTCCCCCTCCGACGGCTCCCTTCAACCTG
GCGGACATCAACGACGTGAGCCCCTCGGGCGGCTTCGTGGCCGAGCTCCTGCGGCCAGAATTGGACCCGGTGTACATTCC
GCCGCAGCAGCCGCAGCCGCCAGGTGGCGGGCTGATGGGCAAGTTCGTGCTGAAGGCGTCGCTGAGCGCCCCTGGCGGCG
AGTACGGCAGCCCGTCGGTCATCAGCGTCGGCAAAGGCAGCCCTGACGGCAGCCACCCGGTGGTGGTGGCGCCCTACAAC
GGCGGGCCGCCGCGCACGTGTCCCAAGATCAAGCAGGAGGCGGTCTCCTCGTGCACCCACTTGGGCGCTGGACCCCCTCT
CAGCAATGGCCACCGGCCGGCTGCACACGACCTCCCCCTGGGGCGGCAGCTCCCCAGCAGGACTACCCCGACCCTGGGTC
TTGAGGCAGTGCTGAGCAGCAGGGACTGTCACCCTGCCCTGCCGCTTCCCCCCGGCTTCCATCCCCACCTAGGGCCCAAT
TACCCATCCTTCCTGCCCGACCAGATGCAGCCGCTCCACTACCAAGAGCTCATGCCACCTGGTTGGTGCATGCCGGAGGA
GCCCAAGCCAAAGAGGGGAAGACGATCGTGGCCCCGGAAAAGGACCGCCACCCACACTTGTGATTACGCGGGCTGCGGCA
AAACCTACACAGAGTTCTCA

Alignment

ORF - retro_pabe_2020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.12 %
• Parental protein coverage: 85.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRQPPGESDMAVSDALLPSFSTFASGPAGREKTLRQAGAPNNRWREELSHMKRLPPVLPGRPYDLAAATV
          MRQPPGESDMAVSDALLPSFSTFASGPAGREKTLRQAGAPNNRWREELSHMKRLPPVLPGRPYDLAAATV
Retrocopy MRQPPGESDMAVSDALLPSFSTFASGPAGREKTLRQAGAPNNRWREELSHMKRLPPVLPGRPYDLAAATV

Parental  ATDLESGGAGAACGGSNLVPLPRRETEEFNDLLDLDFILSNSLTHPPESVAATVSSSASASSSSSPSSSG
          ATDLESGGAGAACGGSNL.PLPRRETEEFNDLLDLDFILSNSLTHPPESVAATVSSSASASSSSSPSSSG
Retrocopy ATDLESGGAGAACGGSNLAPLPRRETEEFNDLLDLDFILSNSLTHPPESVAATVSSSASASSSSSPSSSG

Parental  PASAPSTCSFTYPIRAGNDPGVAPGGTGGGLLY-GRESAPPPTAPFNLADINDVSPSGGFVAELLRPELD
          PASAPSTCSFTYPIRAGNDPGVAPGGTGG.LL..GRESAPPPTAPFNLADINDVSPSGGFVAELLRPELD
Retrocopy PASAPSTCSFTYPIRAGNDPGVAPGGTGGDLLM<GRESAPPPTAPFNLADINDVSPSGGFVAELLRPELD

Parental  PVYIPPQQPQPPGGGLMGKFVLKASLSAPGSEYGSPSVISVSKGSPDGSHPVVVAPYNGGPPRTCPKIKQ
          PVYIPPQQPQPPGGGLMGKFVLKASLSAPG.EYGSPSVISV.KGSPDGSHPVVVAPYNGGPPRTCPKIKQ
Retrocopy PVYIPPQQPQPPGGGLMGKFVLKASLSAPGGEYGSPSVISVGKGSPDGSHPVVVAPYNGGPPRTCPKIKQ

Parental  EAVSSCTHLGAGPPLSNGHRPAAHDFPLGRQLPSRTTPTLGLEEVLSSRDCHPALPLPPGFHPHPGPNYP
          EAVSSCTHLGAGPPLSNGHRPAAHD.PLGRQLPSRTTPTLGLE.VLSSRDCHPALPLPPGFHPH.GPNYP
Retrocopy EAVSSCTHLGAGPPLSNGHRPAAHDLPLGRQLPSRTTPTLGLEAVLSSRDCHPALPLPPGFHPHLGPNYP

Parental  SFLPDQMQPQVPPLHYQELMPPGSCMPEEPKPKRGRRSWPRKRTATHTCDYAGCGKTYTKSS
          SFLPDQMQP....LHYQELMPPG.CMPEEPKPKRGRRSWPRKRTATHTCDYAGCGKTYT..S
Retrocopy SFLPDQMQP----LHYQELMPPGWCMPEEPKPKRGRRSWPRKRTATHTCDYAGCGKTYTEFS

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	1.38 RPM
SRP007412_cerebellum	0.00 RPM	0.85 RPM
SRP007412_heart	0.00 RPM	3.76 RPM
SRP007412_kidney	0.00 RPM	1.96 RPM
SRP007412_liver	0.00 RPM	1.53 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2020 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2020 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2020 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020355	1 retrocopy	retro_btau_521,
Pongo abelii	ENSPPYG00000013114	1 retrocopy	retro_pabe_2384,
Pongo abelii	ENSPPYG00000019478	7 retrocopies	retro_pabe_1836, retro_pabe_2020 , retro_pabe_2022, retro_pabe_2024, retro_pabe_2027, retro_pabe_2037, retro_pabe_3579,
Rattus norvegicus	ENSRNOG00000016299	1 retrocopy	retro_rnor_2164,
Ictidomys tridecemlineatus	ENSSTOG00000022002	1 retrocopy	retro_itri_1862,