RetrogeneDB ID: retro_hsap_3825

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:22550233..22551618(-)
• Located in intron of: ENSG00000105889

Retrocopy information

• Ensembl ID: ENSG00000233476
• 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_3825
ATGGGAAAGGAAAAGACTCATATCAACATTGTCGTCATTGGACACGTAGATTCAGGCAAGTCCACCACTACTGGCCATCT
GATCTATAAATGCGGTGGCATCGACAAAAGAACCATTGAAAAATTTGAGAAGGAGGCTGCTGAGATGGGAAAGGGCTCCT
TCAAGTATGCCTGGGTCTTGGATAAACTGAAAGCTGAGCGTGAACGTGGTATCACCATTGATATCTCCTTGTGGAAATTT
GAGACCAGCAAGTACTATGTGACTATCATTGATGCCCCAGGACACAGGGACTTCATCAAAAACATGATTACAGGGACATC
TCAGGCTGACTGTGCTGTCCTGATTGTTGCTGCTGGTGTTGGTGAATTTGAAGCTGGTATCTCCAAGAATGGGCAGACCC
GAGAGCATGCCCTTCTGGCTTACACACTGGGTGTGAAACAACTAATTGTCGGTGTTAACAAAATGGATTCCACTGAGCCA
CCCTACAGCCAGAAGAGATATGAGGAAATTGTTAAGGAATCAGCACTTACATTAAGAAAATTGGCTACAACCCCGACACA
GTAGCATTTGTGCCAATTTCTGGTTGGAATGGTGACAACATGCTGGAGCCAAGTGCTAACATGCCTTGGTTCAAGGGATG
GAAAGTCACCCGTAAGGATGGCAATGCCAGTGGAACCACGCTGCTTGAGGCTCTGGACTGCATCCTACCACCAACTCATC
CAACTGACAAGCCCTTGCGCCTGCCTCTCCAGGATGTCTACAAAATTGGTGGTATTGGTACTGTTCCTGTTGGCCGAGTG
GAGACTGGTGTTCTCAAACCCGGTATGGTGGTCACCTTTGCTCCAGTCAACGTTACAACGGAAGTAAAATCTGTCGAAAT
GCACCATGAAGCTTTGAGTGAAGCTCTTCCTGGGGACAATGTGGGCTTCAATGTCAAGAATGTGTCTGTCAAGGATGTTC
GTCGTGGCAACGTCGCTGGTGACAGCAAAAATGACCCACCAATGGAAGCAGCGGGCTTCACTGCTCAGGTGATTATCCTG
AACCATCCAGGCCAAATAAGCACCGGCTATGCCCCTGTATTGGATTGCCACACGGCTCACATTGCATGCAAGTTTGCTGA
GCTGAAGGAAAAGATTGATCGCCGTTCTGGTAAAAAGCTGGAAGATGGCCCTAAATTCTTGAAGTCTGGTGATGCTGCCA
TTGTTGATATGGTTCCTGGCAAGCCCATGTGTGTTGAGAGCTTCTCAGACTATCCACCTTTGGGTCGCTTTGCTGTTCGT
GATATGAGACAGACAGTTGCGGTGGGTGTCATCAAAGCAGTGGACAAGAAGGCTGCTGGAGCTGGCAAGGTCACCAAGTC
TGCCCAGAAAGCTCAGAAGGCTAAA

Alignment

ORF - retro_hsap_3825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.14 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
          MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
Retrocopy MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG

Parental  ITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA
          ITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA
Retrocopy ITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA

Parental  YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKE-VSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMP
          YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKE..STYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMP
Retrocopy YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKE<ISTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMP

Parental  WFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVT
          WFKGWKVTRKDGNASGTTLLEALDCILPPT.PTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVT
Retrocopy WFKGWKVTRKDGNASGTTLLEALDCILPPTHPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVT

Parental  FAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNH
          FAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNH
Retrocopy FAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNH

Parental  PGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYP
          PGQIS.GYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYP
Retrocopy PGQISTGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYP

Parental  PLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
          PLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
Retrocopy PLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK

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	2.15 RPM	5264.08 RPM
bodymap2_adrenal	3.34 RPM	4408.93 RPM
bodymap2_brain	0.98 RPM	1165.02 RPM
bodymap2_breast	2.16 RPM	3630.18 RPM
bodymap2_colon	3.87 RPM	6218.58 RPM
bodymap2_heart	0.30 RPM	698.42 RPM
bodymap2_kidney	1.63 RPM	2811.08 RPM
bodymap2_liver	0.46 RPM	1314.04 RPM
bodymap2_lung	2.71 RPM	6336.68 RPM
bodymap2_lymph_node	3.02 RPM	5735.42 RPM
bodymap2_ovary	5.67 RPM	7786.50 RPM
bodymap2_prostate	4.57 RPM	8544.31 RPM
bodymap2_skeletal_muscle	1.05 RPM	972.29 RPM
bodymap2_testis	1.51 RPM	3096.81 RPM
bodymap2_thyroid	2.30 RPM	4724.61 RPM
bodymap2_white_blood_cells	4.88 RPM	9598.56 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3825 was not detected

EST

No EST(s) were mapped for retro_hsap_3825 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_173852	83 libraries	39 libraries	574 libraries	695 libraries	438 libraries

The graphical summary, for retro_hsap_3825 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_3825 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3825 has 0 orthologous retrocopies within eutheria group .

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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,