RetrogeneDB ID: retro_pabe_1135

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:83254645..83255278(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3L
• Ensembl ID: ENSPPYG00000011806
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit L [Source:HGNC Symbol;Acc:18138]

Sequence

>retro_pabe_1135
AGTGATGTCATTGACCAGAAGGTGTATAGGATCCAGGACATCTATGAGAACAGCTGGACCAAGCTGACTGAAAGATTCTT
CAAAAATACACCTTGGCCCGAGGCTGAAGCCATTGCTCCACAAGTTGGCAACAATGCTGTCTTCCTGGTTTTATATAAAG
AATTATACTACAGACACATATATGCCAAAGTCAGTGGGAGACCTTCCTTGGAGCAGAAGTTTGAATCCTGTTATAACAAT
TGCAATCTCTTCAACTACATTCTTAATGTTGATGGTCCTCCTTCCCTTGAACTACCCAACCAGGGGCTCTAGCATATCAT
TGATGAGTTCATCTACCAGTTTCAGTCATTCAGTCAGTACTGCTATAAGACTGCCAAGAAGTCGGAGGAGGAGATTGACT
TCCTTTGTTCCAATCCCAAAATCTGGAATGTTCACAGTGTCCTCAATGTCCTTCATTCCTTCGTAGACAAATCCAACATC
AACCGACAGTTGGAGATGTACACAAGCGGAGGTGACTGTGAGAGTGTGGCTAGGGAGATGCTTGGTTACTTCAGCCTGGT
GGGTCTTCTCTGCCTGCACTCCCTGTTAGGAGATTAGTACCAGGCCATCAAGGTGCTGGAGAACATCGAGCTG

Alignment

ORF - retro_pabe_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.11 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDLIDQKVYELQASRVSSDWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKELYYRHIYAKVSGGPS
          SD.IDQKVY..Q.....S.WTKLTERFFKNTPWPEAEAIAPQVGN.AVFL.LYKELYYRHIYAKVSG.PS
Retrocopy SDVIDQKVYRIQDIYENS-WTKLTERFFKNTPWPEAEAIAPQVGNNAVFLVLYKELYYRHIYAKVSGRPS

Parental  LEQRFESYYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQYRCKTAKKSEEEIDFLRSNP
          LEQ.FES.YN.CNLFNYILN.DGP..LELPNQ.L..IIDEFIYQFQSFSQY..KTAKKSEEEIDFL.SNP
Retrocopy LEQKFESCYNNCNLFNYILNVDGPPSLELPNQGL*HIIDEFIYQFQSFSQYCYKTAKKSEEEIDFLCSNP

Parental  KIWNVHSVLNVLHSLVDKSNINRQLEVYTSGSMYSRVPECQVTTYYYVGFAYL--MMRRYQDAIRVFANI
          KIWNVHSVLNVLHS.VDKSNINRQLE.YTSG.....V..........VG...L.........AI.V..NI
Retrocopy KIWNVHSVLNVLHSFVDKSNINRQLEMYTSGGDCESVAREMLGYFSLVGLLCLHSLLGD*YQAIKVLENI

Parental  LL
          .L
Retrocopy EL

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	38.43 RPM
SRP007412_cerebellum	0.00 RPM	56.54 RPM
SRP007412_heart	0.00 RPM	46.75 RPM
SRP007412_kidney	0.00 RPM	75.81 RPM
SRP007412_liver	0.00 RPM	53.77 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1135 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1135 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1135 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_940

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001443	3 retrocopies	retro_cfam_1496, retro_cfam_1877, retro_cfam_315,
Monodelphis domestica	ENSMODG00000019068	3 retrocopies	retro_mdom_1247, retro_mdom_1585, retro_mdom_432,
Otolemur garnettii	ENSOGAG00000029444	1 retrocopy	retro_ogar_1635,
Pongo abelii	ENSPPYG00000011806	2 retrocopies	retro_pabe_1135 , retro_pabe_1136,
Pteropus vampyrus	ENSPVAG00000010103	1 retrocopy	retro_pvam_648,