RetrogeneDB ID: retro_hsap_615

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:98510044..98510653(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000236552
• Aliases: RPL13AP5, RPL13A_8_1086, bA196N24.2
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL13A
• Ensembl ID: ENSG00000142541
• Aliases: RPL13A, L13A, TSTA1
• Description: ribosomal protein L13a [Source:HGNC Symbol;Acc:10304]

Sequence

>retro_hsap_615
ATGGCGGAGGTGCAGGTCCTGGTGCTTGATGGTCGAGGCCATCTCCTGGGCCGCCTGGCGGCCATCGTGGCTAAACAGGT
ACTGCTGGGCCGGAAGGTGGTGGTTGTACGCTGTGAAGGCATCAACATTTCTGGCAATTTCTACAGAAACAAGTTGAAGT
ACCTGGCTTTCCTCCGCAAGCGGATGAACACCAACCCTTCCCGAGTCCCCTACCACTTCCGGGCCCCCAGCCGCATCTTC
TGGCGGACCGTGCGAGGTATGCTGCCCCACAAGACCAAGCGAGGCCAGGCCGCTCTGGACCGTCTCAAGGTGTTTGACGG
CATCCCACCGCCCTACGACAAGAAAAAGCGGATGGTGGTTCCTGCTGCCCTCAAGGTCGTGCGTCTGAAGCCTACAAGAA
AGTTTGCCTATCTGGGGCGCCTGGCTCACGAGGTTGGCTGGAAGTACCAGGCAGTGACAGCCACCCTGGAGGAGAAGAGG
AAAGAGAAAGCCAAGATCCACTACCGGAAGAAGAAACAGCTCATGAGGCTACGGAAACAGGCCGAGAAGAACGTGGAGAA
GAAAATTGACAAATACACAGAGGTCCTCAAGACCCACGGACTCCTGGTC

Alignment

ORF - retro_hsap_615 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEVQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPSRGP
          MAEVQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPSR.P
Retrocopy MAEVQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPSRVP

Parental  YHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGR
          YHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGR
Retrocopy YHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGR

Parental  LAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGLLV
          LAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGLLV
Retrocopy LAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGLLV

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
bodymap2_adipose	4.31 RPM	967.42 RPM
bodymap2_adrenal	8.56 RPM	1518.40 RPM
bodymap2_brain	0.94 RPM	156.35 RPM
bodymap2_breast	3.11 RPM	689.11 RPM
bodymap2_colon	4.04 RPM	1303.66 RPM
bodymap2_heart	0.79 RPM	269.24 RPM
bodymap2_kidney	1.59 RPM	446.76 RPM
bodymap2_liver	0.93 RPM	328.33 RPM
bodymap2_lung	3.59 RPM	1095.62 RPM
bodymap2_lymph_node	4.62 RPM	1494.82 RPM
bodymap2_ovary	6.88 RPM	1466.56 RPM
bodymap2_prostate	6.63 RPM	1422.20 RPM
bodymap2_skeletal_muscle	5.51 RPM	598.29 RPM
bodymap2_testis	2.19 RPM	649.24 RPM
bodymap2_thyroid	2.92 RPM	674.57 RPM
bodymap2_white_blood_cells	4.69 RPM	1717.29 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_615 was not detected

EST

No EST(s) were mapped for retro_hsap_615 retrocopy.

TSS

No TSS is located nearby retro_hsap_615 retrocopy 5' end.

Lab

retro_hsap_615 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_615 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005296	3 retrocopies	retro_btau_1251, retro_btau_719, retro_btau_789,
Canis familiaris	ENSCAFG00000029892	3 retrocopies	retro_cfam_1772, retro_cfam_924, retro_cfam_976,
Callithrix jacchus	ENSCJAG00000000072	16 retrocopies	retro_cjac_1130, retro_cjac_1706, retro_cjac_182, retro_cjac_197, retro_cjac_1997, retro_cjac_2170, retro_cjac_2322, retro_cjac_2467, retro_cjac_2468, retro_cjac_2665, retro_cjac_2699, retro_cjac_2755, retro_cjac_3009, retro_cjac_664, retro_cjac_941, retro_cjac_972,
Echinops telfairi	ENSETEG00000017076	2 retrocopies	retro_etel_46, retro_etel_853,
Homo sapiens	ENSG00000142541	22 retrocopies	retro_hsap_1072, retro_hsap_1100, retro_hsap_1111, retro_hsap_1268, retro_hsap_1410, retro_hsap_2200, retro_hsap_2500, retro_hsap_293, retro_hsap_298, retro_hsap_3173, retro_hsap_3350, retro_hsap_3444, retro_hsap_3652, retro_hsap_3752, retro_hsap_3772, retro_hsap_397, retro_hsap_436, retro_hsap_615 , retro_hsap_671, retro_hsap_730, retro_hsap_753, retro_hsap_967,
Loxodonta africana	ENSLAFG00000016213	3 retrocopies	retro_lafr_1160, retro_lafr_576, retro_lafr_810,
Mus musculus	ENSMUSG00000074129	3 retrocopies	retro_mmus_1129, retro_mmus_1334, retro_mmus_20,
Pteropus vampyrus	ENSPVAG00000010958	3 retrocopies	retro_pvam_129, retro_pvam_625, retro_pvam_771,
Rattus norvegicus	ENSRNOG00000020618	10 retrocopies	retro_rnor_1073, retro_rnor_1112, retro_rnor_1212, retro_rnor_1292, retro_rnor_1357, retro_rnor_1742, retro_rnor_564, retro_rnor_593, retro_rnor_665, retro_rnor_988,
Sus scrofa	ENSSSCG00000003166	4 retrocopies	retro_sscr_290, retro_sscr_300, retro_sscr_392, retro_sscr_743,