RetrogeneDB ID: retro_mmus_3433

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:33505660..33507007(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000079297
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eif2s3x
• Ensembl ID: ENSMUSG00000035150
• Aliases: Eif2s3x, AA409828, AA547477, AI314668, Eif-2gx
• Description: eukaryotic translation initiation factor 2, subunit 3, structural gene X-linked [Source:MGI Symbol;Acc:MGI:1349431]

Sequence

>retro_mmus_3433
GATGTTACCAAGTTGACACCACTTTCACATGAAGTTATCAGCAGACAAGCTACAATTAATATTGGTACAATTGGTCACGT
AGCTCATGGGAAGTCCACTGTGGTGAAGGCTATTTCTGGAGTTCACACTGTCAGATTCAAAAATGAACTCGAAAGGAACA
TTACCATCAAGCTTGGATATGCTAATGCTAAGATTTATAAACTTGATGACCCAAGTTGTCCTAGACCAGAATGTTACAGA
TCGTGTGGAAGCAGCACACCAGATGAGTTTCCTACAGACATTCCGGGGACCAAAGGGAACTTCAAGTTAGTCAGGCATGT
TTCCTTTGTTGACTGTCCTGGCCATGATATTTTGATGGCTACGATGCTGAACGGTGCAGCAGTGATGGATGCGGCCCTTC
TGTTGATAGCTGGTAACGAATCATGCCCTCAGCCCCAGACTTCCGAACACCTGGCTGCCATAGAAATCATGAAACTCAAG
CATATTTTGATCTTACAGAATAAAATTGATCTGGTAAAAGAAAGTCAGGCTAAGGAACAATATGAGCAAATCCTCGCATT
TGTGCAAGGAACCGTAGCAGAAGGGGCACCAATTATTCCAATTTCTGCTCAACTGAAGTACAATATTGAAGTTGTCTGTG
AGTATATAGTGAAGAAAATACCAGTGCCCCCAAGAGACTTTACTTCAGAGCCCCGTCTCATTGTCATCAGGTCATTTGAT
GTCAACAAACCTGGCTGTGAAGTCGATGACCTTAAGGGAGGTGTAGCTGGTGGTAGTATCCTAAAAGGAGTGTTAAAGGT
AGGCCAGGAGATAGAAGTGAGACCCGGTATTGTCTCCAAAGACAGTGAAGGAAAACTCATGTGTAAACCAATCTTTTCCA
AAATTGTGTCACTTTTTGCGGAACATAATGATCTTCAATATGCTGCCCCGGGTGGTCTCATTGGAGTTGGAACAAAGATC
GACCCCACCTTGTGCCGAGCTGACAGAATGGTGGGACAAGTGCTCGGTGCAGTTGGAGCTTTACCTGAAATATTCACCGA
ACTGGAGATTTCCTATTTCCTGCTTAGACGTCTTCTGGGTGTACGTACTGAAGGAGACAAGAAAGCAGCAAAGGTCCAAA
AGCTGTCTAAGAATGAAGTGCTTATGGTCAACATAGGCTCCCTGTCGACAGGAGGAAGAGTTAGTGCAGTCAAGGCTGAT
TTGGGCAAAATTGTTTTGACCAATCCCGTGTGCACAGAAGTAGGAGAAAAAATTGCCCTTAGCAGAAGAGTTGAGAAACA
CTGGCGTTTAATTGGTTGGGGTCAGATAAGAAGAGGAGTGACCATTAAGCCAACTGTAGATGATGAC

Alignment

ORF - retro_mmus_3433 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 95.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELERNITIKLGYANAKIYKLDD
          DVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELERNITIKLGYANAKIYKLDD
Retrocopy DVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELERNITIKLGYANAKIYKLDD

Parental  PSCPRPECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNE
          PSCPRPECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNE
Retrocopy PSCPRPECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNE

Parental  SCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQLKYNIE
          SCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQLKYNIE
Retrocopy SCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQLKYNIE

Parental  VVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQEIEVRPGIVSK
          VVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQEIEVRPGIVSK
Retrocopy VVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQEIEVRPGIVSK

Parental  DSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGAVGALPEIFTELEI
          DSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGAVGALPEIFTELEI
Retrocopy DSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGAVGALPEIFTELEI

Parental  SYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPVCTEVGEKIAL
          SYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPVCTEVGEKIAL
Retrocopy SYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPVCTEVGEKIAL

Parental  SRRVEKHWRLIGWGQIRRGVTIKPTVDDD
          SRRVEKHWRLIGWGQIRRGVTIKPTVDDD
Retrocopy SRRVEKHWRLIGWGQIRRGVTIKPTVDDD

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	0.37 RPM	14.09 RPM
SRP007412_cerebellum	0.13 RPM	11.98 RPM
SRP007412_heart	0.44 RPM	19.83 RPM
SRP007412_kidney	0.31 RPM	16.38 RPM
SRP007412_liver	0.16 RPM	15.54 RPM
SRP007412_testis	0.05 RPM	1.01 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3433 was not detected

EST

14 EST(s) were mapped to retro_mmus_3433 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA684005	33505668	33506080	100	412	0	412
AA690260	33505736	33506212	97.9	466	10	456
BF138695	33505659	33506209	98.7	529	6	518
BY158944	33506019	33506434	99.6	411	2	407
BY161110	33506019	33506388	99.8	368	1	367
BY172211	33506019	33506493	98.9	340	4	335
CA326634	33505709	33506416	99.6	697	3	693
CA886180	33506207	33506618	100	411	0	411
CF532037	33505568	33506241	100	673	0	673
CF533735	33505785	33506331	100	546	0	546
CK344150	33505615	33506297	100	682	0	682
CK345766	33505746	33506338	100	592	0	592
CN525671	33505690	33506401	99.9	707	0	704
CN529648	33505856	33506488	100	631	0	631

TSS

No TSS is located nearby retro_mmus_3433 retrocopy 5' end.

Lab

retro_mmus_3433 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3433 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
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,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Ictidomys tridecemlineatus	ENSSTOG00000007144	1 retrocopy	retro_itri_582,