RetrogeneDB ID: retro_ggor_1448

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 19:42343866..42344358(+)
• Located in intron of: ENSGGOG00000008674

Retrocopy information

• Ensembl ID: ENSGGOG00000023351
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF5A
• Ensembl ID: ENSGGOG00000012032
• Aliases: None
• Description: None

Sequence

>retro_ggor_1448
TTGCGAGAATTGGAATCGAAGCCTCTTAAAATGGCAGATGATTTGGACTTCGAGACAAGAGATGCAGGGGCCTCGGCCTC
CTTCCCAATGCAGTGCTCAGCATTATGTAACACTGGCTTTGTGGTGCTCAAAGGCTGGCCCTGTAAGGTCTTTGAGATGT
CTGCTTGGAAGACTGGCAAGCACGGCCGCGCCAAGGTCCACCTGGTTGGTATTGACATCTTTACTGGGAAGAAATATAAA
AATAACTGCCTGTCACCTTATAATGTGGGTGTCCCCAACATCAAAAGGAATGACTCCCAGCTGATTGGCATCCAGGAAGG
TACCCCTCACTGCTCCAGGACAGCAGGGAGGTGCGAGAGGACCTTCTTCGTCTGCCAGAGGAGACCTTGGCAAGGAGATG
AGCAGAAGTACCGCTGTGGAGAAGGGACCCTGATCACCGTGCTGTCTGCCATGACAGAGGAGGCAGCTGTTGCAGTCAAG
GCCATGGCAAAA

Alignment

ORF - retro_ggor_1448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.76 %
• Parental protein coverage: 89.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKRLESKPLKMADDLDFETGDAGASATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVG
          L..LESKPLKMADDLDFET.DAGASA.FPMQCSAL...GFVVLKG.PCK..EMS..KTGKHG.AKVHLVG
Retrocopy LRELESKPLKMADDLDFETRDAGASASFPMQCSALCNTGFVVLKGWPCKVFEMSAWKTGKHGRAKVHLVG

Parental  IDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGIQDG-YLSLLQDSGEVRED-LRLPE-GDLGKEI-EQK
          IDIFTGKKY...C.S..N..VPNIKRND.QLIGIQ.G.Y.SLLQDS.EVRED.LRLPE.GDLGKE..EQK
Retrocopy IDIFTGKKYKNNCLSPYNVGVPNIKRNDSQLIGIQEG<YPSLLQDSREVREDLLRLPE<GDLGKEM<EQK

Parental  YDCGEEILITVLSAMTEEAAVAIKAMAK
          Y.CGE..LITVLSAMTEEAAVA.KAMAK
Retrocopy YRCGEGTLITVLSAMTEEAAVAVKAMAK

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	0.19 RPM	102.24 RPM
SRP007412_cerebellum	0.32 RPM	88.76 RPM
SRP007412_heart	0.03 RPM	66.79 RPM
SRP007412_kidney	0.08 RPM	119.68 RPM
SRP007412_liver	0.05 RPM	123.74 RPM
SRP007412_testis	0.00 RPM	181.61 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1448 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1448 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2004
Pongo abelii	retro_pabe_1640
Macaca mulatta	retro_mmul_1379

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132507	3 retrocopies	retro_hsap_1788, retro_hsap_2004, retro_hsap_9,
Gorilla gorilla	ENSGGOG00000012032	2 retrocopies	retro_ggor_1448 , retro_ggor_159,
Microcebus murinus	ENSMICG00000012459	1 retrocopy	retro_mmur_711,
Macaca mulatta	ENSMMUG00000006206	1 retrocopy	retro_mmul_1379,
Monodelphis domestica	ENSMODG00000006652	2 retrocopies	retro_mdom_1641, retro_mdom_190,
Otolemur garnettii	ENSOGAG00000014230	1 retrocopy	retro_ogar_2414,
Pongo abelii	ENSPPYG00000007907	1 retrocopy	retro_pabe_1468,
Pan troglodytes	ENSPTRG00000008674	3 retrocopies	retro_ptro_1198, retro_ptro_442, retro_ptro_504,
Rattus norvegicus	ENSRNOG00000016478	3 retrocopies	retro_rnor_1627, retro_rnor_1947, retro_rnor_671,
Sus scrofa	ENSSSCG00000017939	1 retrocopy	retro_sscr_1204,
Tursiops truncatus	ENSTTRG00000009783	1 retrocopy	retro_ttru_1526,