RetrogeneDB ID: retro_pabe_1828

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:45503515..45503810(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRM
• Ensembl ID: ENSPPYG00000001892
• Aliases: None
• Description: spermidine synthase [Source:HGNC Symbol;Acc:11296]

Sequence

>retro_pabe_1828
GATGTCATCCAAGTCTCTAGGAAGTTCCTGCCAGGCATGGCCAGTTGCTACTCTAGTTCAAAGCTGACCCTTCATGTGGA
TGACGTTTTGAGTTCATGAAGCAGAACTAGGATGTCTTCGATGTTATCACTGACTTCCCAGACCACATGGGCCCGGCTGA
AAGCCTCTTCAAGGAAGCCTATTGTCAGCGGATGAAGGTGAAGATGGCCCTCGAGGAGGATGGCATTCTCTGCTGCCAGG
GAGAGCGCCAGTGGCTGCACCTTCACCTCATAAGGAGATGCGGCAGTTCTGCCAG

Alignment

ORF - retro_pabe_1828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.45 %
• Parental protein coverage: 56.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DVIQVSKKFLPGMAIGYSSSKLTLHVGD-GFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKT-
          DVIQVS.KFLPGMA..YSSSKLTLHV.D..FEFMKQN.D.FDV.ITD..D.MGPAESLFKE.Y.Q.MK..
Retrocopy DVIQVSRKFLPGMASCYSSSKLTLHVDD<RFEFMKQN*DVFDV-ITDFPDHMGPAESLFKEAYCQRMKVK

Parental  -ALKEDGVLCCQGECQWLHLDLI-KEMRQFCQ
          .AL.EDG.LCCQGE.QWLHL.LI.KEMRQFCQ
Retrocopy MALEEDGILCCQGERQWLHLHLI<KEMRQFCQ

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	38.26 RPM
SRP007412_cerebellum	0.00 RPM	6.69 RPM
SRP007412_heart	0.00 RPM	6.41 RPM
SRP007412_kidney	0.03 RPM	16.18 RPM
SRP007412_liver	0.00 RPM	15.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1828 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1828 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1828 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002354	4 retrocopies	retro_cjac_2131, retro_cjac_2524, retro_cjac_3331, retro_cjac_4025,
Homo sapiens	ENSG00000116649	2 retrocopies	retro_hsap_1426, retro_hsap_2313,
Gorilla gorilla	ENSGGOG00000014385	1 retrocopy	retro_ggor_1756,
Macropus eugenii	ENSMEUG00000007002	2 retrocopies	retro_meug_1330, retro_meug_887,
Macaca mulatta	ENSMMUG00000019321	2 retrocopies	retro_mmul_1500, retro_mmul_2259,
Nomascus leucogenys	ENSNLEG00000009532	3 retrocopies	retro_nleu_1842, retro_nleu_2082, retro_nleu_2778,
Pongo abelii	ENSPPYG00000001892	3 retrocopies	retro_pabe_1181, retro_pabe_1828 , retro_pabe_2044,
Pan troglodytes	ENSPTRG00000000138	3 retrocopies	retro_ptro_1403, retro_ptro_1688, retro_ptro_975,