RetrogeneDB ID: retro_hsap_4931

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: Y:5205788..5207005(-)
• Located in intron of: ENSG00000099715

Retrocopy information

• Ensembl ID: ENSG00000235001
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSG00000161960
• Aliases: EIF4A1, DDX2A, EIF-4A, EIF4A, eIF-4A-I, eIF4A-I
• Description: eukaryotic translation initiation factor 4A1 [Source:HGNC Symbol;Acc:3282]

Sequence

>retro_hsap_4931
ATGTCTGTGAGCCAGGATTCCTGATCCAGAGACAATGGCCCCGATGGGATGGAGCCCGAATGCGTCATTGAGAGTAACTG
GAATGAGATTGTTGACAGCTTTGATGACATGAACCTCTCGGAGTCCCTTCTCCGTGACATCTATGCCTATGGTTTTGAGA
AGCCCTCTGCCATCCAGCAGCAAGCCATTCTACCTTGTATCAGGGGTTATAATGTAATCGCTCAAGCCCGATCTGGGACT
GGGAAAATGGCCACATTTGCCATATCGATTCTGCAGCAGATTGAATTAGATCTAAAAGCCACCCAGGCCTTGGTCCTAGC
ACCCACTCGAGAATTGGCTCAGCAGATACAGAAGGTGGTCATGGCACTAGTAGACTACATGGGTGCCTCCTGTCATGCCT
GTGTCAGGGGCACCAATATGCGTGCTGAGGTGCAGAAACTGCAGATGGAAGCTCCCCACATCATCGTGGGTACCCCTAGC
CGTGTGTTTGATATGCTTAACCAGAGATACCTGTCTCCCAAATACATCAAGATGTTTGTACTGGATAAAGCTGATGAAAT
GTTAAGCCGTGGATTCAAGGACCAGATCTATGACATATTCCAAAAGCTCAACAGCAACACCCAGGTAGTTTTGCTGTCAG
CTACAATGCCTTCTGATATGCTTGAGGTGATCAAGAAGTTCATGAGGGACCCCATTCGGATTCTTGTCAAGAAGGAAGAG
TTGACCCTGGAGGGCATCCGCCAATTCTACATCAACGTGGAACAAGAGGAGTGGAAGCTGGACACACTATGTGACTTGTA
TGAAACCCTGACCATCACCCAGGAAGTCATCTTCATCAACACCCGGAGGAAGGTGGACTGGCTCACTGAGAAGATGCATG
CTCGAGATTTCACTGTCTCCGCCATGCATGGAGATATGGACCAAAAGGAGCAAGACGTGATCATGAGGGAGTTTCATTCT
GGCTCTAGCAGAGTTTTGATTACAACTGACCTGCTGGCCAGAGGCATTGATGTGCAGCAGGTTTCTTTAGTCATCAACTA
TGACCTTCCCACCAACAGGGAAAACTATATCCACAGAATCAGTCGAGGTGGACGGTTTGGCCGTAAAGGTGTGGCTATTA
ACATGGTGACAGAAGAAGACAAGAGGACTCTTCAAGACATTGAGATCTTCTACAACACCTCCATTGAGGAAATGCCCCCA
ATGTTGCTGACCTCATC

Alignment

ORF - retro_hsap_4931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGY
          MS.SQDS.SRDNGPDGMEPE.VIESNWNEIVDSFDDMNLSESLLR.IYAYGFEKPSAIQQ.AILPCI.GY
Retrocopy MSVSQDS*SRDNGPDGMEPECVIESNWNEIVDSFDDMNLSESLLRDIYAYGFEKPSAIQQQAILPCIRGY

Parental  DVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNV
          .VIAQA.SGTGK.ATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMAL.DYMGASCHAC..GTN.
Retrocopy NVIAQARSGTGKMATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALVDYMGASCHACVRGTNM

Parental  RAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV
          RAEVQKLQMEAPHIIVGTP.RVFDMLN.RYLSPKYIKMFVLD.ADEMLSRGFKDQIYDIFQKLNSNTQVV
Retrocopy RAEVQKLQMEAPHIIVGTPSRVFDMLNQRYLSPKYIKMFVLDKADEMLSRGFKDQIYDIFQKLNSNTQVV

Parental  LLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFIN
          LLSATMPSD.LEV.KKFMRDPIRILVKKEELTLEGIRQFYINVE.EEWKLDTLCDLYETLTITQ.VIFIN
Retrocopy LLSATMPSDMLEVIKKFMRDPIRILVKKEELTLEGIRQFYINVEQEEWKLDTLCDLYETLTITQEVIFIN

Parental  TRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP
          TRRKVDWLTEKMHARDFTVSAMHGDMDQKE.DVIMREF.SGSSRVLITTDLLARGIDVQQVSLVINYDLP
Retrocopy TRRKVDWLTEKMHARDFTVSAMHGDMDQKEQDVIMREFHSGSSRVLITTDLLARGIDVQQVSLVINYDLP

Parental  TNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMP-LNVADLI
          TNRENYIHRI.RGGRFGRKGVAINMVTEEDKRTL.DIE.FYNTSIEEMP..NVADLI
Retrocopy TNRENYIHRISRGGRFGRKGVAINMVTEEDKRTLQDIEIFYNTSIEEMP<PNVADLI

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	0.18 RPM	4.06 RPM
bodymap2_adrenal	0.06 RPM	24.05 RPM
bodymap2_brain	0.00 RPM	3.59 RPM
bodymap2_breast	0.06 RPM	7.61 RPM
bodymap2_colon	0.14 RPM	3.27 RPM
bodymap2_heart	0.02 RPM	1.90 RPM
bodymap2_kidney	0.02 RPM	4.74 RPM
bodymap2_liver	0.02 RPM	1.94 RPM
bodymap2_lung	0.04 RPM	11.81 RPM
bodymap2_lymph_node	0.04 RPM	10.49 RPM
bodymap2_ovary	0.08 RPM	12.09 RPM
bodymap2_prostate	0.07 RPM	5.92 RPM
bodymap2_skeletal_muscle	0.02 RPM	1.07 RPM
bodymap2_testis	0.04 RPM	1.85 RPM
bodymap2_thyroid	0.04 RPM	6.67 RPM
bodymap2_white_blood_cells	0.08 RPM	3.11 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4931 was not detected

EST

No EST(s) were mapped for retro_hsap_4931 retrocopy.

TSS

No TSS is located nearby retro_hsap_4931 retrocopy 5' end.

Lab

retro_hsap_4931 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4931 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4873
Pan troglodytes	retro_ptro_3247
Pongo abelii	retro_pabe_3792

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004900	1 retrocopy	retro_cpor_1088,
Erinaceus europaeus	ENSEEUG00000003581	1 retrocopy	retro_eeur_610,
Felis catus	ENSFCAG00000024897	1 retrocopy	retro_fcat_370,
Homo sapiens	ENSG00000156976	2 retrocopies	retro_hsap_593, retro_hsap_878,
Homo sapiens	ENSG00000161960	10 retrocopies	retro_hsap_1004, retro_hsap_1182, retro_hsap_1252, retro_hsap_1270, retro_hsap_1796, retro_hsap_2520, retro_hsap_4836, retro_hsap_4873, retro_hsap_4931 , retro_hsap_610,
Gorilla gorilla	ENSGGOG00000024702	8 retrocopies	retro_ggor_1321, retro_ggor_1572, retro_ggor_3015, retro_ggor_537, retro_ggor_798, retro_ggor_920, retro_ggor_983, retro_ggor_998,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Myotis lucifugus	ENSMLUG00000003415	3 retrocopies	retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Mus musculus	ENSMUSG00000059796	7 retrocopies	retro_mmus_1810, retro_mmus_1853, retro_mmus_2320, retro_mmus_2473, retro_mmus_3122, retro_mmus_325, retro_mmus_527,
Nomascus leucogenys	ENSNLEG00000009547	7 retrocopies	retro_nleu_2109, retro_nleu_2117, retro_nleu_230, retro_nleu_2470, retro_nleu_2769, retro_nleu_440, retro_nleu_701,
Pan troglodytes	ENSPTRG00000008694	10 retrocopies	retro_ptro_1201, retro_ptro_1465, retro_ptro_2954, retro_ptro_3112, retro_ptro_3247, retro_ptro_450, retro_ptro_750, retro_ptro_810, retro_ptro_862, retro_ptro_870,
Rattus norvegicus	ENSRNOG00000030628	3 retrocopies	retro_rnor_1059, retro_rnor_2213, retro_rnor_2306,
Sorex araneus	ENSSARG00000006017	7 retrocopies	retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,
Ictidomys tridecemlineatus	ENSSTOG00000024814	1 retrocopy	retro_itri_610,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	0.26 RPM
CEU_NA11930	0.26 RPM
CEU_NA12004	0.23 RPM
CEU_NA12400	0.14 RPM
CEU_NA12751	0.10 RPM
CEU_NA12760	0.49 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.11 RPM
CEU_NA12873	0.16 RPM
FIN_HG00183	0.30 RPM
FIN_HG00277	0.33 RPM
FIN_HG00315	0.11 RPM
FIN_HG00321	0.15 RPM
FIN_HG00328	0.21 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.54 RPM
FIN_HG00375	0.22 RPM
FIN_HG00377	0.28 RPM
FIN_HG00378	0.15 RPM
GBR_HG00099	0.15 RPM
GBR_HG00111	0.11 RPM
GBR_HG00114	0.18 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.23 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.13 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.19 RPM
GBR_HG00143	0.29 RPM
TSI_NA20512	0.20 RPM
TSI_NA20513	0.22 RPM
TSI_NA20518	0.47 RPM
TSI_NA20532	0.71 RPM
TSI_NA20538	0.37 RPM
TSI_NA20756	0.26 RPM
TSI_NA20765	0.15 RPM
TSI_NA20771	0.14 RPM
TSI_NA20786	0.26 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.34 RPM
YRI_NA18907	0.14 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.16 RPM
YRI_NA19099	0.27 RPM
YRI_NA19114	0.16 RPM
YRI_NA19118	0.06 RPM
YRI_NA19213	0.19 RPM
YRI_NA19214	0.15 RPM
YRI_NA19223	0.26 RPM

---

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).