RetrogeneDB ID: retro_mmul_473

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:28605210..28606629(-)
• Located in intron of: ENSMMUG00000032215

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2S3
• Ensembl ID: ENSMMUG00000006979
• Aliases: None
• Description: None

Sequence

>retro_mmul_473
ATGGCGGGCGGAGAAGCTGGAGTGACTCTGGGGCAGCCGCATCTTTCGCGTCAGGATCTCACCACGTTGGATGTTACCAA
GTTGACGCCACTTTCACACGAAGTTATCAGCAGACAAGCCACAATTAATATAGGTACAATTGGTCATGTAGCTCATGGGA
AATCCACAGTCGTCAAAGCTATTTCTGGAGTTCACACCGTCAGGTTAAAAAATGAACTAGAAAGAAATATTACAATCAAG
CTTGGATTGTAATATGCTAATACTAAGATTTATAAACTTGGTGACCCAAGTTGCCCTCGGCCAGGGTGTTATAGATCTTG
TGGGAGCAGTACACCTGATGAGTTTCCTACAGATATTGCAGGGACAAAAGGGAACTTCAAATCAGTCAGACATGTTTCCT
TTGTTGACTGTCCTGGCCACGATGTTTTGATGGCTACTATGCTGAATGGTGCAGCAGTGATGGATGCAGCTTTTCTGTTG
ATAGCTGGTAATGACTCTTGTCCTCAGCCTCAGACGTCTGAACACCTGGCTGCTATAGAGATCATGAAACTGAAGCATAT
TTTGATTCTACAAAATAAAATTGATTTGGTAAAAGAAAGTCAGGCTAAAGAACAATACGAGCAGATCCTTGCATTTGTCT
AAGGTACAGTAGCAGAGTTAGCTCCCATTATTCCAATTTTGGCTCAGCTGAAATACAATATTGAAGTTGTTTGTGAGTAC
ATAGTAAAGAAAATTCCAGTATCCCCAAGAGACTTTACTTCAGAGCCCGGGCTTATTGTTATTAAATCTTTTGATGTCGA
CAAACCTGGCTGTGAAGTTGATGACCTTAATGGAGGTGTAGCTGGTGGTAGTATCCTAAAAGGAGTATTAACGGTGGACC
AGGAGATAGAAGTAAGACCTGGTATTGTTTCCAAAGATAGTGAAGGAAAACTCATGTGTAAACCAATCTTTTCCAAAATT
GTATCACTTTTTGCAGAGCATAATGATCTGTAATATGCTGCTCCAGGCAGTCTTACTGGAGTTGGAACAAAAATTGACCC
CACTTTGGGCCGGGCTGACAGAATGGTGGGGCAAGTACTTGGTACAGTCAGAGCTTTACCTGAGATATTCACAGAATTGG
AAATTTCCTATTTCCTGCTTAGACGGCTTCTAGGTGTATGCACTGAAGGAGACAAGAAAGCAGCAAAGGTTCAAAAGCTG
TCTAAGAATGAAGTGCTCATGGTGAACATAGGATCCCTATTGACAGGAGGGAGAGTTAGTGCTGTCAAGGCCGATTTGGG
TAAAATTGTTTTGACCAATCCAGTGTGCACAGAGGTAGGAGAAAAAATTGCCCTTAGCCGAAGAGTTGAAAAACACTGGC
GTTTAATTGGTTGGGGTCAGATAAGAGGAGTGACAATCAAGCCAACAGTAGATGATGAC

Alignment

ORF - retro_mmul_473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.88 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFK
          MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVR.K
Retrocopy MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRLK

Parental  NELERNITIKLG--YANAKIYKLDDPSCPRPECYRSCGSSTPDEFPTDIAGTKGNFKLVRHVSFVDCPGH
          NELERNITIKLG..YAN.KIYKL.DPSCPRP.CYRSCGSSTPDEFPTDIAGTKGNFK.VRHVSFVDCPGH
Retrocopy NELERNITIKLGL*YANTKIYKLGDPSCPRPGCYRSCGSSTPDEFPTDIAGTKGNFKSVRHVSFVDCPGH

Parental  DILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQIL
          D.LMATMLNGAAVMDAA.LLIAGN.SCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQIL
Retrocopy DVLMATMLNGAAVMDAAFLLIAGNDSCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQIL

Parental  AFVQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGV
          AFV.GTVAE.APIIPI.AQLKYNIEVVCEYIVKKIPV.PRDFTSEP.LIVI.SFDV.KPGCEVDDL.GGV
Retrocopy AFV*GTVAELAPIIPILAQLKYNIEVVCEYIVKKIPVSPRDFTSEPGLIVIKSFDVDKPGCEVDDLNGGV

Parental  AGGSILKGVLKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLC
          AGGSILKGVL.V.QEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDL.YAAPG.L.GVGTKIDPTL.
Retrocopy AGGSILKGVLTVDQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDL*YAAPGSLTGVGTKIDPTLG

Parental  RADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVS
          RADRMVGQVLG.V.ALPEIFTELEISYFLLRRLLGV.TEGDKKAAKVQKLSKNEVLMVNIGSL.TGGRVS
Retrocopy RADRMVGQVLGTVRALPEIFTELEISYFLLRRLLGVCTEGDKKAAKVQKLSKNEVLMVNIGSLLTGGRVS

Parental  AVKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD
          AVKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQI.RGVTIKPTVDDD
Retrocopy AVKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQI-RGVTIKPTVDDD

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	21.18 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	29.19 RPM
SRP007412_cerebellum	0.13 RPM	25.77 RPM
SRP007412_heart	0.06 RPM	28.32 RPM
SRP007412_kidney	0.23 RPM	19.25 RPM
SRP007412_liver	0.04 RPM	9.94 RPM
SRP007412_testis	0.23 RPM	3.84 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_473 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_473 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_473 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Dasypus novemcinctus	ENSDNOG00000018584	1 retrocopy	retro_dnov_1454,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
Echinops telfairi	ENSETEG00000000341	4 retrocopies	retro_etel_1061, retro_etel_126, retro_etel_1590, retro_etel_2017,
Loxodonta africana	ENSLAFG00000011052	1 retrocopy	retro_lafr_971,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473 , retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650, retro_mdom_732,
Mus musculus	ENSMUSG00000035150	2 retrocopies	retro_mmus_1408, retro_mmus_3433,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10,
Pteropus vampyrus	ENSPVAG00000002533	1 retrocopy	retro_pvam_936,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Ictidomys tridecemlineatus	ENSSTOG00000007144	1 retrocopy	retro_itri_582,
Tursiops truncatus	ENSTTRG00000012474	4 retrocopies	retro_ttru_1080, retro_ttru_1638, retro_ttru_617, retro_ttru_686,