RetrogeneDB ID: retro_mmul_1906

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:127441552..127442937(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MMU.11091
• Ensembl ID: ENSMMUG00000004852
• Aliases: None
• Description: eukaryotic translation elongation factor 1 alpha 1 [Source:RefSeq peptide;Acc:NP_001182679]

Sequence

>retro_mmul_1906
ATAGGAAAGGAAAATATTCATATCAACATTGTCGTCATTGAACACGTACATTCAGTCAGGTCCACCACTACTGGCCATGT
GATCTACAAATGTAGTGGCATCGACAAAAGAACCATTGAAAAATTTGAGAAGGAGGCTGCTGAGATGGGAAAGGGCTCGT
TCAAGTATGCCTGGGTCTTGGGTTAACTGAAAGCTGAGCATGAGCATGGTATCACCATTGATATCTCCTTGTAGAAATCT
GAGACCAGCAAGTACTATGTGGCTATCATTGATGCCCCAGGACACAGAGACTTCATCAAAAACATGATTACAGGGACATC
TCAGGCTGACCGTAATGTTCTGAATGTTGCTGCTGGTGTTGGTGAATTTGAAGCTGGTAACTTCAAAAATGGTCAGACCC
GAGAACATGCCCTTCTGGGTTACACAGTGGGTGTGAAACAACAAATCAATTATGTTAAAAAAATGGATTCCACTGAGCCA
CCGTACAGCCAGAAGTGATATGAGGAAATCATTAAGGAAGTCAGCACTTATATTAAGAAATTGGCTACAACCCCGACACA
GTAGCATTTGTGCCAATTTCTGGTTGGAATGGTGACAACATGCTGGAGCCAAATGCTAACATGCCTTGGTTCAAGACATG
GAAAGTCACCTGAAACGACGGCAATACCAGTGGAAACACGCTGCTTGAGGCTCTGGACTGCATCCAACCACCAACTCGTC
CAACTGACAAGCCCTTGCACCTGCCTCTTCAGGATGCCTACAAAATTGGTGGTATTGGTATTGTTCTTGTAGGTCAACTG
GAGACTGATGTTCTCAAACCCAGTATGGTGGCCACTTTTGCTCCAGTATACATTACAACTGAAGCAAAATCTGTTGAAAT
GCATCATGAAGCTTTAAGTGAAGCTCTTCCTGGGGACATTATGGGCTACAATGTCAAGAATGTGTCTGTTAAGGAAGTTC
ATCATGGCAACATCGCTGGTGACAGCAAAAATGACCCACCAATGGAAGCAGCTGGCTTCACTCCTCAAGTGATTATCCTG
AACCATCCAGGCCAAATCAGTGCTGGCTATGCCCCTGTGCTGGATTGCCAGACGGCTCACATTGCATGCAAGTTTGCTGA
GCTGAAGGAAAAGATTGATCACCGTTCTGGTAAAAAGCTGGAAGATGGCCCTAAATTATTGAGTTCTGGTGATGCTGCCA
TCATTGATATGGTTCCTGGCAAGCCCATGTGTGTTGAGAGCTTCTCATACTATCCACCTCTGCGTCATTTTGCTGTTCGT
GATATGAGACAGACGATTGTCCTGGATGTCATCAAAGGAGTGGACAAGAAGGCTGCCGGAGCTGGCAAGGCCACCAAGTC
TGCCCAGAAAGCTCAGAAGGCCAAA

Alignment

ORF - retro_mmul_1906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
          .GKE..HINIVVI.HV.S..STTTGH.IYKC.GIDKRTIEKFEKEAAEMGKGSFKYAWVL..LKAE.E.G
Retrocopy IGKENIHINIVVIEHVHSVRSTTTGHVIYKCSGIDKRTIEKFEKEAAEMGKGSFKYAWVLG*LKAEHEHG

Parental  ITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA
          ITIDISL.K.ETSKYYV.IIDAPGHRDFIKNMITGTSQAD..VL.VAAGVGEFEAG..KNGQTREHALL.
Retrocopy ITIDISL*KSETSKYYVAIIDAPGHRDFIKNMITGTSQADRNVLNVAAGVGEFEAGNFKNGQTREHALLG

Parental  YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKK-IGYNPDTVAFVPISGWNGDNMLEPSANMP
          YT.GVKQ.I..V.KMDSTEPPYSQK.YEEI.KEVSTYIKK.IGYNPDTVAFVPISGWNGDNMLEP.ANMP
Retrocopy YTVGVKQQINYVKKMDSTEPPYSQK*YEEIIKEVSTYIKK<IGYNPDTVAFVPISGWNGDNMLEPNANMP

Parental  WFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVT
          WFK.WKVT..DGN.SG.TLLEALDCI.PPTRPTDKPL.LPLQD.YKIGGIG.V.VG..ET.VLKP.MV.T
Retrocopy WFKTWKVT*NDGNTSGNTLLEALDCIQPPTRPTDKPLHLPLQDAYKIGGIGIVLVGQLETDVLKPSMVAT

Parental  FAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNH
          FAPV..TTE.KSVEMHHEALSEALPGD..G.NVKNVSVK.V..GN.AGDSKNDPPMEAAGFT.QVIILNH
Retrocopy FAPVYITTEAKSVEMHHEALSEALPGDIMGYNVKNVSVKEVHHGNIAGDSKNDPPMEAAGFTPQVIILNH

Parental  PGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYP
          PGQISAGYAPVLDC.TAHIACKFAELKEKID.RSGKKLEDGPK.L.SGDAAI.DMVPGKPMCVESFS.YP
Retrocopy PGQISAGYAPVLDCQTAHIACKFAELKEKIDHRSGKKLEDGPKLLSSGDAAIIDMVPGKPMCVESFSYYP

Parental  PLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
          PL..FAVRDMRQT....VIK.VDKKAAGAGK.TKSAQKAQKAK
Retrocopy PLRHFAVRDMRQTIVLDVIKGVDKKAAGAGKATKSAQKAQKAK

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	0.11 RPM	257.72 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	933.00 RPM
SRP007412_cerebellum	0.13 RPM	305.24 RPM
SRP007412_heart	0.12 RPM	637.02 RPM
SRP007412_kidney	0.47 RPM	964.42 RPM
SRP007412_liver	1.11 RPM	1738.88 RPM
SRP007412_testis	0.11 RPM	580.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1906 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1906 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1906 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2983
Gorilla gorilla	retro_ggor_2066

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
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	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
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,
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,
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,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,