RetrogeneDB ID: retro_hsap_3314

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:43495177..43496230(-)
• Located in intron of: ENSG00000172244

Retrocopy information

• Ensembl ID: ENSG00000249855
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EEF1A1
• Ensembl ID: ENSG00000156508
• Aliases: EEF1A1, CCS-3, CCS3, EE1A1, EEF-1, EEF1A, EF-Tu, EF1A, GRAF-1EF, HNGC:16303, LENG7, PTI1, eEF1A-1
• Description: eukaryotic translation elongation factor 1 alpha 1 [Source:HGNC Symbol;Acc:3189]

Sequence

>retro_hsap_3314
TGTGCTGTCCTGATGGTTGCTGCTGGTGTTGGCGAATTTGAAACTGGTATCTCCAAGAATGGGCAGACCTGAGAGCATGC
CCTTCTGGCTTACACACTGGGTGTGAAACAACTAATTGTTGGTGTTAACAAAATGGATTCCACTGAGCCACCCTACAGCC
AGAAGAGAGAAGAGGAAATTGTTAAGGAAGTCAGCACTTACATTAAGAAAATTGGTTACAACCCTGACACAGTAGCATTT
GTGCCAATTTCTGGTTGGAATGGTGACAACATGCTGGAGCCGAGTGCTAACATGCCTTGGCTCAAGGGATGGAAAGCCAC
CCGTAAGGATGGCAGTGCCAGCGGCACCATGCTGCTTGAGGCTCTGGACTGCATCCTACCACCAACTCATCCAACTGACA
AGCCCTTGCGCCTGCCTCTCCAGGATGTCTACAAAATTGGTGGTATTGGTACTGTTCCTGTTGGCCGAGTGGAGACTGGT
GTTCTCAAACCTGGTGTGGTGGTCACCTTTGCTCCAGTCAACATTACAACAGAAGTAAAATCTGTCGAAATGCACCATGA
AGCTTTGAGTGAAGCTCTTCCTGGGGACAATGTGGGCTTCAATGTCAAGAATGTGTCTGTCAAGGATGTTCGTCGTGGCA
ACGTTGCTGGTGACAGCAAAAATGACCCACCAATGGAAACAGCTGACTTCATTGCTCAGGTAATTATCCTGAACCATCCA
GGCCAAATAAGCGCTGGCTATGCCCCTATATTGGATTGCCACGCGGCTCACATTGCATGCAAGTTTGCTGAGCTGAAGGA
AAAGATTGATCGCGGTTCTGGTAAAAAGCTGGAAGATGGCCCTAAATTCTTGAAGTCTGGTGATGCTGCCATTGTTGATA
TGGTTCCTGGCAAGCCCATTGTTGAGAGCTTCTCAGACTATCCACCTTTGGGTCATTTTGCTGTTCGTGATATGAGACAG
ACAGTTGCGGTGGGTGTCATCAAAGCAGTGGACAAGAAGGCTGCTGGAGGTGGCAAGGTCACGAAGTCTGCCCAGACAGC
TCAGAAGGCTAAA

Alignment

ORF - retro_hsap_3314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 76.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CAVLIVAAGVGEFEAGISKNGQTREHALLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKK
          CAVL.VAAGVGEFE.GISKNGQT.EHALLAYTLGVKQLIVGVNKMDSTEPPYSQKR.EEIVKEVSTYIKK
Retrocopy CAVLMVAAGVGEFETGISKNGQT*EHALLAYTLGVKQLIVGVNKMDSTEPPYSQKREEEIVKEVSTYIKK

Parental  IGYNPDTVAFVPISGWNGDNMLEPSANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPL
          IGYNPDTVAFVPISGWNGDNMLEPSANMPW.KGWK.TRKDG.ASGT.LLEALDCILPPT.PTDKPLRLPL
Retrocopy IGYNPDTVAFVPISGWNGDNMLEPSANMPWLKGWKATRKDGSASGTMLLEALDCILPPTHPTDKPLRLPL

Parental  QDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDV
          QDVYKIGGIGTVPVGRVETGVLKPG.VVTFAPVN.TTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDV
Retrocopy QDVYKIGGIGTVPVGRVETGVLKPGVVVTFAPVNITTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDV

Parental  RRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDG
          RRGNVAGDSKNDPPME.A.F.AQVIILNHPGQISAGYAP.LDCH.AHIACKFAELKEKIDR.SGKKLEDG
Retrocopy RRGNVAGDSKNDPPMETADFIAQVIILNHPGQISAGYAPILDCHAAHIACKFAELKEKIDRGSGKKLEDG

Parental  PKFLKSGDAAIVDMVPGKPMCVESFSDYPPLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQK
          PKFLKSGDAAIVDMVPGKP..VESFSDYPPLG.FAVRDMRQTVAVGVIKAVDKKAAG.GKVTKSAQ.AQK
Retrocopy PKFLKSGDAAIVDMVPGKPI-VESFSDYPPLGHFAVRDMRQTVAVGVIKAVDKKAAGGGKVTKSAQTAQK

Parental  AK
          AK
Retrocopy AK

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	1.53 RPM	5264.08 RPM
bodymap2_adrenal	1.86 RPM	4408.93 RPM
bodymap2_brain	0.52 RPM	1165.02 RPM
bodymap2_breast	1.17 RPM	3630.18 RPM
bodymap2_colon	2.15 RPM	6218.58 RPM
bodymap2_heart	0.04 RPM	698.42 RPM
bodymap2_kidney	1.18 RPM	2811.08 RPM
bodymap2_liver	0.11 RPM	1314.04 RPM
bodymap2_lung	0.30 RPM	6336.68 RPM
bodymap2_lymph_node	0.91 RPM	5735.42 RPM
bodymap2_ovary	1.14 RPM	7786.50 RPM
bodymap2_prostate	0.95 RPM	8544.31 RPM
bodymap2_skeletal_muscle	0.25 RPM	972.29 RPM
bodymap2_testis	0.81 RPM	3096.81 RPM
bodymap2_thyroid	0.96 RPM	4724.61 RPM
bodymap2_white_blood_cells	1.67 RPM	9598.56 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3314 was not detected

EST

No EST(s) were mapped for retro_hsap_3314 retrocopy.

TSS

No TSS is located nearby retro_hsap_3314 retrocopy 5' end.

Lab

retro_hsap_3314 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3314 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1305

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 126 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014534	3 retrocopies	retro_btau_114, retro_btau_115, retro_btau_192,
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Equus caballus	ENSECAG00000020363	2 retrocopies	retro_ecab_66, retro_ecab_93,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Felis catus	ENSFCAG00000030977	14 retrocopies	retro_fcat_1021, retro_fcat_1388, retro_fcat_1569, retro_fcat_1683, retro_fcat_1825, retro_fcat_184, retro_fcat_1915, retro_fcat_220, retro_fcat_221, retro_fcat_334, retro_fcat_515, retro_fcat_566, retro_fcat_688, retro_fcat_737,
Homo sapiens	ENSG00000156508	27 retrocopies	retro_hsap_1093, retro_hsap_1181, retro_hsap_1567, retro_hsap_1671, retro_hsap_190, retro_hsap_2302, retro_hsap_2455, retro_hsap_2637, retro_hsap_2712, retro_hsap_278, retro_hsap_283, retro_hsap_2896, retro_hsap_2920, retro_hsap_2967, retro_hsap_2983, retro_hsap_3239, retro_hsap_3291, retro_hsap_3314 , retro_hsap_363, retro_hsap_3701, retro_hsap_3706, retro_hsap_3758, retro_hsap_3825, retro_hsap_3917, retro_hsap_4220, retro_hsap_4730, retro_hsap_989,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Myotis lucifugus	ENSMLUG00000013537	24 retrocopies	retro_mluc_110, retro_mluc_1252, retro_mluc_1392, retro_mluc_1430, retro_mluc_1558, retro_mluc_1628, retro_mluc_1644, retro_mluc_1853, retro_mluc_1901, retro_mluc_1910, retro_mluc_2071, retro_mluc_2148, retro_mluc_2154, retro_mluc_2277, retro_mluc_2355, retro_mluc_2358, retro_mluc_2359, retro_mluc_2391, retro_mluc_441, retro_mluc_470, retro_mluc_677, retro_mluc_950, retro_mluc_956, retro_mluc_966,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mustela putorius furo	ENSMPUG00000003816	6 retrocopies	retro_mputfur_1514, retro_mputfur_1643, retro_mputfur_220, retro_mputfur_502, retro_mputfur_844, retro_mputfur_862,
Mustela putorius furo	ENSMPUG00000004271	10 retrocopies	retro_mputfur_1179, retro_mputfur_1276, retro_mputfur_1351, retro_mputfur_1394, retro_mputfur_284, retro_mputfur_355, retro_mputfur_474, retro_mputfur_678, retro_mputfur_920, retro_mputfur_973,
Oryctolagus cuniculus	ENSOCUG00000008481	3 retrocopies	retro_ocun_1102, retro_ocun_187, retro_ocun_71,
Ochotona princeps	ENSOPRG00000016685	6 retrocopies	retro_opri_1049, retro_opri_1076, retro_opri_1197, retro_opri_298, retro_opri_325, retro_opri_383,
Sus scrofa	ENSSSCG00000004489	4 retrocopies	retro_sscr_169, retro_sscr_492, retro_sscr_612, retro_sscr_758,
Tursiops truncatus	ENSTTRG00000000114	19 retrocopies	retro_ttru_1020, retro_ttru_1150, retro_ttru_1196, retro_ttru_1349, retro_ttru_1351, retro_ttru_1368, retro_ttru_1384, retro_ttru_1810, retro_ttru_1861, retro_ttru_1876, retro_ttru_384, retro_ttru_390, retro_ttru_401, retro_ttru_523, retro_ttru_664, retro_ttru_698, retro_ttru_844, retro_ttru_941, retro_ttru_998,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.73 RPM
CEU_NA11843	1.25 RPM
CEU_NA11930	0.95 RPM
CEU_NA12004	0.46 RPM
CEU_NA12400	0.74 RPM
CEU_NA12751	0.95 RPM
CEU_NA12760	0.85 RPM
CEU_NA12827	0.94 RPM
CEU_NA12872	0.93 RPM
CEU_NA12873	1.37 RPM
FIN_HG00183	1.13 RPM
FIN_HG00277	0.96 RPM
FIN_HG00315	1.02 RPM
FIN_HG00321	1.45 RPM
FIN_HG00328	1.14 RPM
FIN_HG00338	0.57 RPM
FIN_HG00349	0.57 RPM
FIN_HG00375	0.88 RPM
FIN_HG00377	0.58 RPM
FIN_HG00378	0.70 RPM
GBR_HG00099	0.35 RPM
GBR_HG00111	0.71 RPM
GBR_HG00114	0.68 RPM
GBR_HG00119	1.44 RPM
GBR_HG00131	0.92 RPM
GBR_HG00133	0.72 RPM
GBR_HG00134	1.14 RPM
GBR_HG00137	0.82 RPM
GBR_HG00142	1.36 RPM
GBR_HG00143	1.12 RPM
TSI_NA20512	0.51 RPM
TSI_NA20513	1.55 RPM
TSI_NA20518	0.67 RPM
TSI_NA20532	1.26 RPM
TSI_NA20538	0.74 RPM
TSI_NA20756	0.96 RPM
TSI_NA20765	1.16 RPM
TSI_NA20771	0.91 RPM
TSI_NA20786	0.39 RPM
TSI_NA20798	0.44 RPM
YRI_NA18870	0.95 RPM
YRI_NA18907	0.52 RPM
YRI_NA18916	0.93 RPM
YRI_NA19093	0.34 RPM
YRI_NA19099	0.51 RPM
YRI_NA19114	0.50 RPM
YRI_NA19118	0.56 RPM
YRI_NA19213	0.84 RPM
YRI_NA19214	0.54 RPM
YRI_NA19223	0.80 RPM

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Indel association:

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