RetrogeneDB ID: retro_pabe_2011

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:87862103..87862454(-)
• Located in intron of: ENSPPYG00000012599

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL36A
• Ensembl ID: ENSPPYG00000025837
• Aliases: None
• Description: ribosomal protein L36a [Source:HGNC Symbol;Acc:10359]

Sequence

>retro_pabe_2011
ATTACTTTCCGTGCCAATAGCGCTCACGCAAACATGGTGAACATCCCTAAAACCCGCAGGACTTTCTGTAAGAAGTGTAG
CAAGCAACCAAACCTGCAAAGTGACACAGTACAAGAAGGGCAAGGATTCTCTGTATGCCCAGGGAAAGCGGTGTTATACA
GGAAGCAGAGTGACTATGGTGGGCAAACTAAGCTGATTTTCCAGAAAAAGGCTAAAACTACAAAGAAGATTGTGCTAAGG
CTTCAGTGCGTTGAGCCCAACTGTAGATCTAAGAGAATGCTGGCTATTAAAAGATGCAAGCATTTTGAACTGGGAGGAGA
TAAGAAGAGAAAGGGCCAAGTGACCCAGTTC

Alignment

ORF - retro_pabe_2011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.87 %
• Parental protein coverage: 82.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSFRADSAHASMVNVPKTRRTFCKKCGK-HQPHKVTQYKKGKDSLYAQGKRRYD-RKQSGYGGQTKPIFR
          ..FRA.SAHA.MVN.PKTRRTFCKKC.K..Q..KVTQYKKGKDSLYAQGKR.Y..RKQS.YGGQTK.IF.
Retrocopy ITFRANSAHANMVNIPKTRRTFCKKCSK>NQTCKVTQYKKGKDSLYAQGKRCYT<RKQSDYGGQTKLIFQ

Parental  KKAKTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVIQF
          KKAKTTKKIVLRL.CVEPNCRSKRMLAIKRCKHFELGGDKKRKGQV.QF
Retrocopy KKAKTTKKIVLRLQCVEPNCRSKRMLAIKRCKHFELGGDKKRKGQVTQF

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	34.50 RPM
SRP007412_cerebellum	0.00 RPM	31.74 RPM
SRP007412_heart	0.00 RPM	34.71 RPM
SRP007412_kidney	0.07 RPM	57.97 RPM
SRP007412_liver	0.03 RPM	56.18 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2011 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2011 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2011 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2083

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 91 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008503	1 retrocopy	retro_acar_98,
Callithrix jacchus	ENSCJAG00000004864	4 retrocopies	retro_cjac_304, retro_cjac_353, retro_cjac_55, retro_cjac_72,
Equus caballus	ENSECAG00000015464	9 retrocopies	retro_ecab_129, retro_ecab_131, retro_ecab_204, retro_ecab_219, retro_ecab_265, retro_ecab_268, retro_ecab_294, retro_ecab_543, retro_ecab_646,
Homo sapiens	ENSG00000241343	14 retrocopies	retro_hsap_1477, retro_hsap_1508, retro_hsap_1595, retro_hsap_1782, retro_hsap_2, retro_hsap_2015, retro_hsap_2274, retro_hsap_2632, retro_hsap_3461, retro_hsap_3819, retro_hsap_3981, retro_hsap_4154, retro_hsap_4299, retro_hsap_647,
Monodelphis domestica	ENSMODG00000025578	2 retrocopies	retro_mdom_1878, retro_mdom_971,
Mus musculus	ENSMUSG00000079435	1 retrocopy	retro_mmus_4,
Pongo abelii	ENSPPYG00000025837	37 retrocopies	retro_pabe_1141, retro_pabe_1174, retro_pabe_121, retro_pabe_1226, retro_pabe_1256, retro_pabe_1311, retro_pabe_141, retro_pabe_1463, retro_pabe_1539, retro_pabe_154, retro_pabe_1540, retro_pabe_1616, retro_pabe_1650, retro_pabe_1651, retro_pabe_1944, retro_pabe_195, retro_pabe_2011 , retro_pabe_2331, retro_pabe_2443, retro_pabe_2622, retro_pabe_2857, retro_pabe_296, retro_pabe_3057, retro_pabe_3151, retro_pabe_3273, retro_pabe_3372, retro_pabe_3687, retro_pabe_3704, retro_pabe_441, retro_pabe_449, retro_pabe_55, retro_pabe_573, retro_pabe_574, retro_pabe_667, retro_pabe_73, retro_pabe_772, retro_pabe_931,
Pteropus vampyrus	ENSPVAG00000001569	1 retrocopy	retro_pvam_17,
Rattus norvegicus	ENSRNOG00000011494	1 retrocopy	retro_rnor_259,
Sarcophilus harrisii	ENSSHAG00000013479	1 retrocopy	retro_shar_467,
Ictidomys tridecemlineatus	ENSSTOG00000027251	20 retrocopies	retro_itri_1171, retro_itri_1189, retro_itri_1364, retro_itri_1405, retro_itri_1471, retro_itri_161, retro_itri_1681, retro_itri_290, retro_itri_385, retro_itri_430, retro_itri_555, retro_itri_609, retro_itri_644, retro_itri_730, retro_itri_753, retro_itri_784, retro_itri_803, retro_itri_845, retro_itri_865, retro_itri_903,