RetrogeneDB ID: retro_mmus_1864

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:28862908..28863707(-)
• Located in intron of: ENSMUSG00000024935

Retrocopy information

• Ensembl ID: ENSMUSG00000089993
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eef1a1
• Ensembl ID: ENSMUSG00000037742
• Aliases: None
• Description: eukaryotic translation elongation factor 1 alpha 1 [Source:MGI Symbol;Acc:MGI:1096881]

Sequence

>retro_mmus_1864
ATGGGAAAGGAAAAGACTCGCATCAACATCGTCGTAATCGGACTCGTAGATTCCTGCAAGTCCACCACAACCGGCCACCT
GATCTACAAATGTGGTGGAATTGACAAGCGAACCATCAAAAAGTTTGAGAAGGAGGCTGCTGAGATGGGAAAGGGCTCCT
TCAAGTACGCCGGGTCTTGGACAAACTGAAAGCTGAGCGGGAGTGTGGTATCACTACTGACATCTCCCTGTGGAAATTCA
AGACCAGCGAATACTACGTGACCATCATTGATGCCCCAGGACAAAGAGACTTCATCAAAAACATGACTACAGGCACATCC
CAGGCTGACTGTGCTGTCCTGATTGTTGCTGCTGGTGTTGGTGAATTTGAAGCTGGTATCTCCAAGAACGGGCAGACCCC
TGAGCATGTTCTTCTGGCTTACACCCTGGGTGTGGAACAGCTAACTGTCAGCGTCAATGAAATGGATTCTCCAAGCCACC
ATACAGTCAGAAGAGATACGAGGAAATCGTTAAGGAAGTCAGCACCTACATGAAGAAAATTGGCTACAACCCTGACACAG
TGGCATTTGTGCCAATTTCTGGTTGGAGTGGTGACAACATGCTGGAGCCAGGTGCTAATATGCCTTGGTTCAAGGGATGG
AAAGTCACCCGCAAAGATGGCAGTGCCAGTGGCACCACGCAGCTGGAAGCTTTGGGTTATATCCCGCCACCAACTCGTCC
AACTGACAAGCCTCTGCGACTGCCCCTCCAGGATGTCTATAAAATTGGGGGCATTGGCACTGTCCCCGTGGGCCGAGTG

Alignment

ORF - retro_mmus_1864 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.59 %
• Parental protein coverage: 57.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAW-VLDKLKAERER
          MGKEKT.INIVVIG.VDS.KSTTTGHLIYKCGGIDKRTI.KFEKEAAEMGKGSFKYA..VLDKLKAERE.
Retrocopy MGKEKTRINIVVIGLVDSCKSTTTGHLIYKCGGIDKRTIKKFEKEAAEMGKGSFKYAG<VLDKLKAEREC

Parental  GITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALL
          GIT.DISLWKF.TS.YYVTIIDAPG.RDFIKNM.TGTSQADCAVLIVAAGVGEFEAGISKNGQT.EH.LL
Retrocopy GITTDISLWKFKTSEYYVTIIDAPGQRDFIKNMTTGTSQADCAVLIVAAGVGEFEAGISKNGQTPEHVLL

Parental  AYTLGVKQLIVGVNKMDS-TEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANM
          AYTLGV.QL.V.VN.MDS...PPYSQKRYEEIVKEVSTY.KKIGYNPDTVAFVPISGW.GDNMLEP.ANM
Retrocopy AYTLGVEQLTVSVNEMDS<SKPPYSQKRYEEIVKEVSTYMKKIGYNPDTVAFVPISGWSGDNMLEPGANM

Parental  PWFKGWKVTRKDGSASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRV
          PWFKGWKVTRKDGSASGTT.LEAL..I.PPTRPTDKPLRLPLQDVYKIGGIGTVPVGRV
Retrocopy PWFKGWKVTRKDGSASGTTQLEALGYIPPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRV

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
SRP007412_brain	0.07 RPM	938.67 RPM
SRP007412_cerebellum	0.09 RPM	652.71 RPM
SRP007412_heart	0.12 RPM	465.27 RPM
SRP007412_kidney	0.40 RPM	1781.75 RPM
SRP007412_liver	0.19 RPM	2430.48 RPM
SRP007412_testis	0.41 RPM	1060.92 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1864 was not detected

EST

No EST(s) were mapped for retro_mmus_1864 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_63399	302 libraries	506 libraries	252 libraries	9 libraries	3 libraries

The graphical summary, for retro_mmus_1864 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 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_mmus_1864 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1864 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 226 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007786	14 retrocopies	retro_amel_1064, retro_amel_1072, retro_amel_1079, retro_amel_1140, retro_amel_1167, retro_amel_1203, retro_amel_1227, retro_amel_1283, retro_amel_1371, retro_amel_160, retro_amel_1742, retro_amel_1797, retro_amel_1855, retro_amel_200,
Bos taurus	ENSBTAG00000014534	3 retrocopies	retro_btau_114, retro_btau_115, retro_btau_192,
Canis familiaris	ENSCAFG00000012222	1 retrocopy	retro_cfam_1478,
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Callithrix jacchus	ENSCJAG00000010051	6 retrocopies	retro_cjac_1431, retro_cjac_3075, retro_cjac_34, retro_cjac_3735, retro_cjac_733, retro_cjac_97,
Cavia porcellus	ENSCPOG00000004067	15 retrocopies	retro_cpor_1150, retro_cpor_1162, retro_cpor_1191, retro_cpor_1256, retro_cpor_1393, retro_cpor_1492, retro_cpor_1499, retro_cpor_348, retro_cpor_381, retro_cpor_387, retro_cpor_413, retro_cpor_709, retro_cpor_891, retro_cpor_918, retro_cpor_959,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000020363	2 retrocopies	retro_ecab_66, retro_ecab_93,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Echinops telfairi	ENSETEG00000004236	14 retrocopies	retro_etel_1189, retro_etel_1248, retro_etel_1260, retro_etel_1429, retro_etel_1436, retro_etel_1472, retro_etel_1578, retro_etel_1602, retro_etel_1682, retro_etel_1808, retro_etel_2135, retro_etel_366, retro_etel_411, retro_etel_830,
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,
Gorilla gorilla	ENSGGOG00000025675	20 retrocopies	retro_ggor_1193, retro_ggor_1258, retro_ggor_1305, retro_ggor_1444, retro_ggor_1529, retro_ggor_20, retro_ggor_2006, retro_ggor_2021, retro_ggor_2056, retro_ggor_2066, retro_ggor_2205, retro_ggor_2526, retro_ggor_2637, retro_ggor_2826, retro_ggor_322, retro_ggor_375, retro_ggor_790, retro_ggor_860, retro_ggor_919, retro_ggor_978,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Microcebus murinus	ENSMICG00000015319	21 retrocopies	retro_mmur_1027, retro_mmur_1116, retro_mmur_1145, retro_mmur_1182, retro_mmur_1190, retro_mmur_12, retro_mmur_1282, retro_mmur_1316, retro_mmur_1339, retro_mmur_1343, retro_mmur_1350, retro_mmur_1568, retro_mmur_171, retro_mmur_26, retro_mmur_273, retro_mmur_49, retro_mmur_682, retro_mmur_729, retro_mmur_825, retro_mmur_877, retro_mmur_9,
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,
Macaca mulatta	ENSMMUG00000004852	15 retrocopies	retro_mmul_1375, retro_mmul_1407, retro_mmul_1518, retro_mmul_1525, retro_mmul_1690, retro_mmul_1707, retro_mmul_1721, retro_mmul_1739, retro_mmul_1743, retro_mmul_1906, retro_mmul_2196, retro_mmul_2250, retro_mmul_323, retro_mmul_6, retro_mmul_848,
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,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864 , retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Nomascus leucogenys	ENSNLEG00000001476	6 retrocopies	retro_nleu_1492, retro_nleu_1584, retro_nleu_1754, retro_nleu_1901, retro_nleu_235, retro_nleu_829,
Oryctolagus cuniculus	ENSOCUG00000008481	3 retrocopies	retro_ocun_1102, retro_ocun_187, retro_ocun_71,
Otolemur garnettii	ENSOGAG00000009152	10 retrocopies	retro_ogar_1215, retro_ogar_1622, retro_ogar_1779, retro_ogar_1840, retro_ogar_2281, retro_ogar_2526, retro_ogar_2557, retro_ogar_3013, retro_ogar_3046, retro_ogar_3271,
Pongo abelii	ENSPPYG00000016777	1 retrocopy	retro_pabe_12,
Pan troglodytes	ENSPTRG00000018347	1 retrocopy	retro_ptro_71,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Vicugna pacos	ENSVPAG00000007637	9 retrocopies	retro_vpac_369, retro_vpac_404, retro_vpac_510, retro_vpac_511, retro_vpac_523, retro_vpac_544, retro_vpac_582, retro_vpac_592, retro_vpac_606,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,