RetrogeneDB ID: retro_rnor_1627

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:107731398..107731769(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eif5a
• Ensembl ID: ENSRNOG00000016478
• Aliases: None
• Description: Eukaryotic translation initiation factor 5A-1 [Source:UniProtKB/Swiss-Prot;Acc:Q3T1J1]

Sequence

>retro_rnor_1627
ATGGCAGATGATTTGGACTTCAAGACAGGAGATGCAGAGGCCCCAGCCACCTTCCCAATGCAGTGTCCAGCATCATGTAA
GAATAGTTTTGTGGTGCTCAAGGGCCAGCCATGTAAGATTGTCGAGATGTCTACTTTGAAAACTGGCAAAGATGGCCATG
CCAAGTTCTATCTGGTTGGTATTGATATTTTTACTGGAAAGAAATCTAAAGATATCTGCCTGTCGACTCATACATGGATG
CCCCAAAAATCAAAAGGAATGACTTCCAGCTGATTGACACCCAAGATGGGTACCTACCCCTGCTCCAGGACAGTGGGGAG
GTACAAGAGCACCTTCATTTGCCTGAGGGAGATTTTGACAAGGAGATTGAA

Alignment

ORF - retro_rnor_1627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.4 %
• Parental protein coverage: 80.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADDLDFETGDAGASATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYE
          MADDLDF.TGDA.A.ATFPMQC.A..KN.FVVLKG.PCKIVEMST.KTGK.GHAK..LVGIDIFTGKK..
Retrocopy MADDLDFKTGDAEAPATFPMQCPASCKNSFVVLKGQPCKIVEMSTLKTGKDGHAKFYLVGIDIFTGKKSK

Parental  DICPSTHN-MDVPNIKRNDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGKEIE
          DIC.STH..MD.P.IKRNDFQLI..QDGYL.LLQDSGEV.E.L.LPEGD..KEIE
Retrocopy DICLSTHT<MDAPKIKRNDFQLIDTQDGYLPLLQDSGEVQEHLHLPEGDFDKEIE

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
SRP017611_brain	0.00 RPM	149.11 RPM
SRP017611_kidney	0.07 RPM	235.38 RPM
SRP017611_liver	0.00 RPM	136.22 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1627 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1627 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1627 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 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,
Macaca mulatta	ENSMMUG00000006206	1 retrocopy	retro_mmul_1379,
Monodelphis domestica	ENSMODG00000006652	2 retrocopies	retro_mdom_1641, retro_mdom_190,
Pongo abelii	ENSPPYG00000007907	1 retrocopy	retro_pabe_1468,
Rattus norvegicus	ENSRNOG00000016478	3 retrocopies	retro_rnor_1627 , retro_rnor_1947, retro_rnor_671,