RetrogeneDB ID: retro_ocun_934

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:18788023..18789177(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSOCUG00000010375
• Aliases: None
• Description: Eukaryotic initiation factor 4A-I [Source:UniProtKB/Swiss-Prot;Acc:P29562]

Sequence

>retro_ocun_934
GTCATTGAGAGTAACTGGAATGAGATCGTTGACAGCTTTGACGACATGAACCTCTCTGAGTCCCTCCTTCGTGGCATCTA
TGCCTATGGTTTTGAGAAGCCCTCTGCCATCCAGCAGCGTGCCATTCTTCCTTGTATCAAGGGTTATGATGTGATCGCTC
AAGCCCAATCTGGGACTGGGAAGACGGCCATATTCGCCATATCGATTCTCCAGCAGATTGAATTGGATCTGAAGGCCACC
CAGGCCTTGGTACTAGCACCCACTCGGGAATTGCCCAACAGATACAAAAGGTGGTCATGGCATTAGGAGATTACATGGGT
GCGTCCTGTCACACCTGCATCGGGGGCACCAATGTGTGTGCTGAGGTGCAGAAGCTGCAAATGGAAGCTCCGCACATAAT
CGTGGGCACCCCTGGCCACGTGTTCGACATGCTTAACCGGAGATACCTGTCTCCCATGTAGATCAAGATGTTTGTACTGG
ACGAAGCTGATGAAATGTTAAGCGGTGGATTCAAGGACCAGATCTATGACCTCTTCCAGAAGCTCAACAGCAACACCCAG
GTGGTTTTGTTGTCAGCTACAGTGCCTTCCGATGTGCTCGAGGTGACCAAGAAGTTCATGAGGGACCCCATCCAGATTCT
TGTCAAGAAGGAGGAGCTGATGCTGGAGGGTATCCGCCAGTTCTACATCAACGTGGAATGCGAGGAGTGGAAGCTGGACA
CACTGTGTGACTTGTACGAGACCCTGACCATAACGCAGGCTGTCATCTTCATCAACACTCAAAGGAAGGTCGATTGGCTC
ACTGAGAAGATGCATGCCCGGGACTTCACCGTCTCTGCCATGCATGGAGATGTGGACCAAAAGGAGCGAGATGTGATCAT
GAGGGAGTTCCACTCTGGCTCTAGCCGAGTACTGATTACCACTGATCTGCTGGCCAGAGGCGTTGATGTACAACAAGTTT
CTTTAGTCATCAACTATGACCTTCCCACCAACAGGGAAAACTATATTCACAGAATTGGCCATGGTGGACGCTTTGACAGT
AAGGGTGTGGCTATTAACATGGTGACAGAAGAAGATAAGCGGACTCTCAGAGACATCGAGACCTTTTACAACACCTCCAT
TGAGGAGATGCCCCTCAATGTTGCTGACCTCATC

Alignment

ORF - retro_ocun_934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.82 %
• Parental protein coverage: 94.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISIL
          VIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTA.FAISIL
Retrocopy VIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTAIFAISIL

Parental  QQIELDLKATQALVLAPTREL-AQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPG
          QQIELDLKATQALVLAPTREL.AQQIQKVVMALGDYMGASCH.CIGGTNV.AEVQKLQMEAPHIIVGTPG
Retrocopy QQIELDLKATQALVLAPTREL<AQQIQKVVMALGDYMGASCHTCIGGTNVCAEVQKLQMEAPHIIVGTPG

Parental  RVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRD
          .VFDMLNRRYLSP..IKMFVLDEADEMLS.GFKDQIYD.FQKLNSNTQVVLLSAT.PSDVLEVTKKFMRD
Retrocopy HVFDMLNRRYLSPM*IKMFVLDEADEMLSGGFKDQIYDLFQKLNSNTQVVLLSATVPSDVLEVTKKFMRD

Parental  PIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVS
          PI.ILVKKEEL.LEGIRQFYINVE.EEWKLDTLCDLYETLTITQAVIFINT.RKVDWLTEKMHARDFTVS
Retrocopy PIQILVKKEELMLEGIRQFYINVECEEWKLDTLCDLYETLTITQAVIFINTQRKVDWLTEKMHARDFTVS

Parental  AMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKG
          AMHGD.DQKERDVIMREF.SGSSRVLITTDLLARG.DVQQVSLVINYDLPTNRENYIHRIG.GGRF..KG
Retrocopy AMHGDVDQKERDVIMREFHSGSSRVLITTDLLARGVDVQQVSLVINYDLPTNRENYIHRIGHGGRFDSKG

Parental  VAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
          VAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
Retrocopy VAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI

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	0.06 RPM	85.60 RPM
SRP017611_kidney	0.10 RPM	143.12 RPM
SRP017611_liver	0.08 RPM	73.91 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_934 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_934 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_934 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000132	1 retrocopy	retro_btau_1207,
Loxodonta africana	ENSLAFG00000001107	1 retrocopy	retro_lafr_1210,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Oryctolagus cuniculus	ENSOCUG00000005011	3 retrocopies	retro_ocun_392, retro_ocun_696, retro_ocun_763,
Oryctolagus cuniculus	ENSOCUG00000010375	5 retrocopies	retro_ocun_1020, retro_ocun_1326, retro_ocun_1375, retro_ocun_475, retro_ocun_934 ,
Pongo abelii	ENSPPYG00000007926	7 retrocopies	retro_pabe_1090, retro_pabe_1474, retro_pabe_3759, retro_pabe_3792, retro_pabe_548, retro_pabe_846, retro_pabe_987,