RetrogeneDB ID: retro_mmus_3200

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:52196063..52197056(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000052825
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Eif2s2
• Ensembl ID: ENSMUSG00000074656
• Aliases: Eif2s2, 2810026E11Rik, 38kDa, AA408636, AA571381, AA986487, AW822225, D2Ertd303e, EIF2, EIF2B
• Description: eukaryotic translation initiation factor 2, subunit 2 (beta) [Source:MGI Symbol;Acc:MGI:1914454]

Sequence

>retro_mmus_3200
ATGTCCGGGGACGAGATGATTTTTGATCCTACTATGAGCAAAAAGAAAAAGAAGAAGAAGAAGCCCTTTATGTTAGATGA
AGAAGGTGATGCCCAGACAGAAGAAACCCAGCCCTCAGAGACAAAAGAAGTGGAGCCAGAACCAACTGAAGAAAAAGACG
TGGACGCTGATGAGGAAGACAGTAGGAAGAAAGATGCTTCTGATGACTTAGATGATTTGAACTTCTTTAATCAAAAGAAA
AAGAAGAAAAAGACGAAAAAGATATTTGACATTGATGAAGCTGAAGAAGCTATAAAGGATGTTAAGATTGAGAGTGATGC
TCAAGAGCCAGCCGAGCCAGAGGATTACCTTGACATTATGCTTGGCAACAAAAAAAAGAAAAAGAAGAATGTTAAATTCC
CAGAAGAAGATGAAATACTAGAAAAAGACGAAGCTTTAGAAGATGAAGACAGCAAAAAAGATGATGGCATTTCATTCAGT
AGCCAAACTGCTTGGGCAGGCTCAGAAAGAGACTACACATATGAGGAGTTGCTGAACCGAGTGTTAAACATCATGAGAGA
AAAGAATCCAGATATGGTTGCTGGAGAGAAGAGGAAATTTGTTATGAAACCTCCACAGGTCATCCGAGTAGGAACCAAGA
AAACTTCTTTTGTCAATTTTACAGATATCTGTAAACTATTACATCGTCAACCCAAACATCTCCTTGCATTTTTATTGGCA
GAATTGGGTACAAGTGGTTCTATAGATGGTAATAACCAACTTGTAATCAAAGGAAGATTCCAACAGAAACAAATAGAAAA
TGTCTTGAGAAGATATATCAAGGAATATGTCACTTGTCACACATGCCGGTCACCGGACACAATCCTACAGAAGGACACCC
GACTCTATTTCTTACAATGTGAAACTTGTCATTCTCGATGCTCTGTTGCCAGTATCAAAACTGGCTTCCAGGCTGTCACA
GGCAAGCGAGCACAGCTCCGTGCCAAAGCTAAC

Alignment

ORF - retro_mmus_3200 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.84 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGDEMIFDPTMSKKKKKKKKPFMLDEEGDAQTEETQPSETKEVEPEPTEEKDVDADEEDSRKKDASDDL
          MSGDEMIFDPTMS........PFMLDEEGDAQTEETQPSETKEVEPEPTEEKDVDADEEDSRKKDASDDL
Retrocopy MSGDEMIFDPTMSXXXXXXXXPFMLDEEGDAQTEETQPSETKEVEPEPTEEKDVDADEEDSRKKDASDDL

Parental  DDLNFFNQKKKKKKTKKIFDIDEAEEAIKDVKIESDAQEPAEPEDDLDIMLGNKKKKKKNVKFPEEDEIL
          DDLNFFN...........FDIDEAEEAIKDVKIESDAQEPAEPED.LDIMLGN.....KNVKFPEEDEIL
Retrocopy DDLNFFNXXXXXXXXXXXFDIDEAEEAIKDVKIESDAQEPAEPEDYLDIMLGNXXXXXKNVKFPEEDEIL

Parental  EKDEALEDEDSKKDDGISFSSQTAWAGSERDYTYEELLNRVFNIMREKNPDMVAGEKRKFVMKPPQVVRV
          EKDEALEDEDSKKDDGISFSSQTAWAGSERDYTYEELLNRV.NIMREKNPDMVAGEKRKFVMKPPQV.RV
Retrocopy EKDEALEDEDSKKDDGISFSSQTAWAGSERDYTYEELLNRVLNIMREKNPDMVAGEKRKFVMKPPQVIRV

Parental  GTKKTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVTCH
          GTKKTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVTCH
Retrocopy GTKKTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVTCH

Parental  TCRSPDTILQKDTRLYFLQCETCHSRCSVASIKTGFQAVTGKRAQLRAKAN
          TCRSPDTILQKDTRLYFLQCETCHSRCSVASIKTGFQAVTGKRAQLRAKAN
Retrocopy TCRSPDTILQKDTRLYFLQCETCHSRCSVASIKTGFQAVTGKRAQLRAKAN

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	26.31 RPM
SRP007412_cerebellum	0.17 RPM	23.53 RPM
SRP007412_heart	0.09 RPM	26.59 RPM
SRP007412_kidney	0.15 RPM	31.09 RPM
SRP007412_liver	0.08 RPM	26.90 RPM
SRP007412_testis	0.18 RPM	50.86 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3200 was not detected

EST

No EST(s) were mapped for retro_mmus_3200 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_142732	298 libraries	426 libraries	326 libraries	16 libraries	6 libraries
TSS #2	TSS_142733	311 libraries	438 libraries	275 libraries	35 libraries	13 libraries
TSS #3	TSS_142734	802 libraries	217 libraries	48 libraries	4 libraries	1 library
TSS #4	TSS_142735	93 libraries	243 libraries	406 libraries	205 libraries	125 libraries

The graphical summary, for retro_mmus_3200 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_3200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3200 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007498	1 retrocopy	retro_cfam_2070,
Choloepus hoffmanni	ENSCHOG00000006521	1 retrocopy	retro_chof_271,
Callithrix jacchus	ENSCJAG00000018334	2 retrocopies	retro_cjac_4196, retro_cjac_697,
Cavia porcellus	ENSCPOG00000015439	1 retrocopy	retro_cpor_1143,
Echinops telfairi	ENSETEG00000001922	1 retrocopy	retro_etel_1101,
Myotis lucifugus	ENSMLUG00000005335	1 retrocopy	retro_mluc_604,
Monodelphis domestica	ENSMODG00000002805	5 retrocopies	retro_mdom_1981, retro_mdom_365, retro_mdom_368, retro_mdom_370, retro_mdom_837,
Mus musculus	ENSMUSG00000074656	1 retrocopy	retro_mmus_3200 ,
Otolemur garnettii	ENSOGAG00000001417	1 retrocopy	retro_ogar_196,
Pongo abelii	ENSPPYG00000010933	2 retrocopies	retro_pabe_1955, retro_pabe_2421,
Rattus norvegicus	ENSRNOG00000017447	1 retrocopy	retro_rnor_2395,
Tupaia belangeri	ENSTBEG00000009970	2 retrocopies	retro_tbel_1505, retro_tbel_2508,