RetrogeneDB ID: retro_hsap_1306

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:22218552..22219827(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000240954
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL4
• Ensembl ID: ENSG00000174444
• Aliases: RPL4, L4
• Description: ribosomal protein L4 [Source:HGNC Symbol;Acc:10353]

Sequence

>retro_hsap_1306
ATGGCATGTGCTTGCCCACTGATGTCAGCGTACTCTGAGAAGGGAGAGTCATCTGGCAAAAATGTCACTTTGTCTGCCAT
ATTCAAGGCTCCTATTCGACCAGATATTGTGAACTTTGTTCACGCCAACTTGTGCAAAAACAACAGACAGCCCTATGCTG
TCAGTGAATCAGCAGGTCATCAAACCAGTGTTGAGTCTTGGAGTACTGGCAGAGCTGCAGCTTGAATTCCCAGAGTTCGA
AGTGGTGGGACTCACCATTCTGGCCAGGGAGCTTTTGGAAACATGTGTCGTGGAGGCTGAATGTTTGCACCAACCAAAAC
CTGGCTCCATTGGCATAGTAGAGTGAATACAACCCCAAAACGATATGTCATCTCTTCTGCCCTGGCTGCCTCAGCCTTAC
CAGCACTGGTTATGTCTAAGGGTCATCGTATTGAGGAAGCTCCTGAACTTCCTTTGGTAGTCGAAGATAAAGTTGAAGGC
TACAAGAAGACCAAGGAGGCTGTTTTGCTTCTTAAGAAACTTAAAGCCTGGAATGATATCGAGAAGGTCTATGTCTCTCA
GCAAATGAGATCCAGCAAGAGCAAAACGAGAAACCATCACCGTATCCGGCGCAGGGGCGCCGCATCATCTGTAATGAGGA
TAATGGTATCGTCAAGGCCTTCAGAAACATCCCTGGAATTACTATGCTTAATATAAGCAAACTGAACATTTTGAAACTTG
CTCCTGGTGGGCATGTGGGACATTTCTGCATTTGGACTCAAAGTGCTTTCTGGAAGTTAGATGAATTTTCTGGCACTTGG
CATAAAGCTGCTTCCCTCAAGAGTAACTACAATCTTCCCATGCACAAGATGATCAATACAGACCTTAGCAGCGTCTTAAA
AAGCCCAGAGATCCAGTGAGCCCTTCGAGCACCTTGCAAGAAGATTCATCGCAGAGTCCTAAAGAACCCACTGAAAAATC
TGAGAATGATGTTGAAGCTAAACCCATACACACAGATCATGCGCCGGAACACCATTCTTCGCTAGGCCAGGAATCACAAA
CTCTGGGTGGATAAGGCAGCAGCCGGCAGCAGCAGCACTAGAAGCCAGATCAGATGAGAAGGGGGTTGTAGGCAAGAAGC
CTGTGGTATGTAAGAAAGGAAAGAAGGCCATTGTTGATGTTAAGAAGCAGAAGAAGCCTCTGGTGGGAGAAAAGGCAGCA
GCTACCAAGAAACCAGCAGCTGAAAAGAAGCCGGCAAAAAAGAAATCTACTACGGAGGAAAAGGAGCCTGCTGCA

Alignment

ORF - retro_hsap_1306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.68 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAESWGTG
          MACA.PL.S.YSEKGESSGKNVTL.A.FKAPIRPDIVNFVH.NL.KNNRQPYAVSE.AGHQTS.ESW.TG
Retrocopy MACACPLMSAYSEKGESSGKNVTLSAIFKAPIRPDIVNFVHANLCKNNRQPYAVSESAGHQTSVESWSTG

Parental  RAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSK
          RA.A.IPRVR.GGTH.SGQGAFGNMCRGG.MFAPTKTW..WH.RVNTT.KRY.I.SALAASALPALVMSK
Retrocopy RAAA*IPRVRSGGTHHSGQGAFGNMCRGG*MFAPTKTWLHWHSRVNTTPKRYVISSALAASALPALVMSK

Parental  GHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRIQRRGPC-I
          GHRIEE.PELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI.KVY.SQ.MR..K.K.RN..RI.RRG...I
Retrocopy GHRIEEAPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIEKVYVSQQMRSSKSKTRNHHRIRRRGAA<I

Parental  IYNEDNGIIKAFRNIPGITLLNVSKLNILKLAPGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNL
          I.NEDNGI.KAFRNIPGIT.LN.SKLNILKLAPGGHVG.FCIWT.SAF.KLDE..GTW.KAASLKSNYNL
Retrocopy ICNEDNGIVKAFRNIPGITMLNISKLNILKLAPGGHVGHFCIWTQSAFWKLDEFSGTWHKAASLKSNYNL

Parental  PMHKMINTDLSRILKSPEIQRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKL
          PMHKMINTDLS..LKSPEIQ.ALRAP.KKIHRRVL.KNPLKNLR.MLKLNPY...MRRNTILR.ARNHKL
Retrocopy PMHKMINTDLSSVLKSPEIQ*ALRAPCKKIHRRVL-KNPLKNLRMMLKLNPYTQIMRRNTILR*ARNHKL

Parental  RVDKAAA-AAAALQAKSDEKAAVAGKKPVVGKKGKKAAVGVKKQKKPLVGKKAAATKKPAPEKKPAEKKP
          .VDKAAA.AAAAL.A.SDEK..V.GKKPVV.KKGKKA.V.VKKQKKPLVG.KAAATKKPA.EKKPA.KK.
Retrocopy WVDKAAA>AAAALEARSDEK-GVVGKKPVVCKKGKKAIVDVKKQKKPLVGEKAAATKKPAAEKKPAKKKS

Parental  TTEEKKPAA
          TTEEK.PAA
Retrocopy TTEEKEPAA

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	0.00 RPM	1176.34 RPM
bodymap2_adrenal	0.41 RPM	1315.18 RPM
bodymap2_brain	0.00 RPM	413.34 RPM
bodymap2_breast	0.02 RPM	811.84 RPM
bodymap2_colon	0.00 RPM	1426.23 RPM
bodymap2_heart	0.00 RPM	355.04 RPM
bodymap2_kidney	0.00 RPM	476.37 RPM
bodymap2_liver	0.00 RPM	408.55 RPM
bodymap2_lung	0.14 RPM	1008.37 RPM
bodymap2_lymph_node	0.66 RPM	1227.00 RPM
bodymap2_ovary	0.10 RPM	1731.25 RPM
bodymap2_prostate	0.19 RPM	1700.57 RPM
bodymap2_skeletal_muscle	0.00 RPM	932.47 RPM
bodymap2_testis	0.04 RPM	864.75 RPM
bodymap2_thyroid	0.00 RPM	937.95 RPM
bodymap2_white_blood_cells	0.49 RPM	1745.21 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1306 was not detected

EST

No EST(s) were mapped for retro_hsap_1306 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_36561	1086 libraries	550 libraries	191 libraries	2 libraries	0 libraries

The graphical summary, for retro_hsap_1306 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_1306 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1306 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_897
Gorilla gorilla	retro_ggor_1023
Macaca mulatta	retro_mmul_2160

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 105 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005211	2 retrocopies	retro_btau_101, retro_btau_610,
Canis familiaris	ENSCAFG00000017309	1 retrocopy	retro_cfam_72,
Choloepus hoffmanni	ENSCHOG00000003008	6 retrocopies	retro_chof_1014, retro_chof_1496, retro_chof_2219, retro_chof_2616, retro_chof_455, retro_chof_476,
Callithrix jacchus	ENSCJAG00000007491	2 retrocopies	retro_cjac_251, retro_cjac_945,
Dasypus novemcinctus	ENSDNOG00000006693	3 retrocopies	retro_dnov_1028, retro_dnov_1152, retro_dnov_1931,
Equus caballus	ENSECAG00000023179	1 retrocopy	retro_ecab_428,
Echinops telfairi	ENSETEG00000000337	3 retrocopies	retro_etel_1876, retro_etel_2195, retro_etel_226,
Felis catus	ENSFCAG00000012293	4 retrocopies	retro_fcat_1136, retro_fcat_189, retro_fcat_505, retro_fcat_567,
Homo sapiens	ENSG00000174444	5 retrocopies	retro_hsap_1306 , retro_hsap_254, retro_hsap_2898, retro_hsap_4229, retro_hsap_471,
Gorilla gorilla	ENSGGOG00000003695	4 retrocopies	retro_ggor_1023, retro_ggor_2008, retro_ggor_2831, retro_ggor_304,
Loxodonta africana	ENSLAFG00000006494	3 retrocopies	retro_lafr_1076, retro_lafr_152, retro_lafr_960,
Microcebus murinus	ENSMICG00000004419	6 retrocopies	retro_mmur_1050, retro_mmur_1330, retro_mmur_440, retro_mmur_562, retro_mmur_830, retro_mmur_852,
Myotis lucifugus	ENSMLUG00000011809	2 retrocopies	retro_mluc_121, retro_mluc_198,
Macaca mulatta	ENSMMUG00000016844	2 retrocopies	retro_mmul_2160, retro_mmul_649,
Monodelphis domestica	ENSMODG00000009657	2 retrocopies	retro_mdom_656, retro_mdom_944,
Mustela putorius furo	ENSMPUG00000000337	3 retrocopies	retro_mputfur_1205, retro_mputfur_411, retro_mputfur_570,
Nomascus leucogenys	ENSNLEG00000012938	4 retrocopies	retro_nleu_1041, retro_nleu_1062, retro_nleu_2385, retro_nleu_887,
Pongo abelii	ENSPPYG00000006578	1 retrocopy	retro_pabe_152,
Pan troglodytes	ENSPTRG00000007195	6 retrocopies	retro_ptro_1512, retro_ptro_1959, retro_ptro_214, retro_ptro_2873, retro_ptro_353, retro_ptro_897,
Pteropus vampyrus	ENSPVAG00000000068	18 retrocopies	retro_pvam_1222, retro_pvam_1342, retro_pvam_201, retro_pvam_202, retro_pvam_216, retro_pvam_236, retro_pvam_267, retro_pvam_399, retro_pvam_428, retro_pvam_430, retro_pvam_435, retro_pvam_466, retro_pvam_518, retro_pvam_736, retro_pvam_778, retro_pvam_819, retro_pvam_865, retro_pvam_955,
Rattus norvegicus	ENSRNOG00000009378	5 retrocopies	retro_rnor_1192, retro_rnor_1621, retro_rnor_2061, retro_rnor_2484, retro_rnor_949,
Sus scrofa	ENSSSCG00000004945	2 retrocopies	retro_sscr_138, retro_sscr_885,
Ictidomys tridecemlineatus	ENSSTOG00000009221	1 retrocopy	retro_itri_437,
Tupaia belangeri	ENSTBEG00000014392	9 retrocopies	retro_tbel_1701, retro_tbel_2186, retro_tbel_2649, retro_tbel_3302, retro_tbel_3577, retro_tbel_3624, retro_tbel_3938, retro_tbel_4340, retro_tbel_4402,
Tarsius syrichta	ENSTSYG00000005588	1 retrocopy	retro_tsyr_1144,
Tursiops truncatus	ENSTTRG00000010206	7 retrocopies	retro_ttru_1130, retro_ttru_1399, retro_ttru_1713, retro_ttru_177, retro_ttru_789, retro_ttru_817, retro_ttru_964,
Vicugna pacos	ENSVPAG00000006746	2 retrocopies	retro_vpac_143, retro_vpac_250,