RetrogeneDB ID: retro_mmus_233

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:22973227..22974514(+)
• Located in intron of: ENSMUSG00000051355

Retrocopy information

• Ensembl ID: ENSMUSG00000044068
• Aliases: Zrsr1, D11Ncvs75, Irlgs2, SP2, U2af1-rs1, U2afbp-rs
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Zrsr2
• Ensembl ID: ENSMUSG00000031370
• Aliases: Zrsr2, 35kDa, 5031411E02Rik, A230052C13Rik, C77286, U2af1-rs2, URP
• Description: zinc finger (CCCH type), RNA binding motif and serine/arginine rich 2 [Source:MGI Symbol;Acc:MGI:103287]

Sequence

>retro_mmus_233
ATGGCATCACGGCAGACCGCGATTCCTGAGAAACTCAGCCGAAAACAATACAAGGCGGCAATGAAGAAGGAGAAACGCAA
GAAACGTCGGCAGAAAATGGCTCGGCTGAGAGCTCTGGAAGCCCCACCAGAGGAGGACGATGATGTTTCTGCTAACGAAG
AACTTGCAGAGCGATTACTGGAGATAGAGCGGCAAAGATTACATGAAGAGTGGCTGCTGAGGGAGGAGAAGGCGCAAGAA
GAATTCAGAATAAAGAAGAAAAAGGAAGAGGCCGCTAGAAAACAGAAGGAAGAACAGGAGAGACAAATAAAGGCCGAGTG
GGAAGAACAACAGAAAAAACAGAGAGAGGAGGAGGAGCAGAAGCTACAGGAGAAGAGAGAGAGGGAGGAAGCGGTGCAGA
AAATGCTGGACCAGGCTGAAAATGAGCGCATTTGGCAGAACCCGGAACCACCCAAGGATTTAAGGCTGGAGAAATATCGA
CCCAGTTGTCCCTTCTACAATAAAACGGGAGCGTGCAGATTTGGTAACAGATGTTCACGGAAACACGACTTTCCCACGTC
AAGTCCCACCCTTCTTGTGAAGAGTATGTTTACAACGTTTGGAATGGAGCAGTGCAGAAGGGATGACTATGACTCAGACG
CAAACCTGGAGTACAGTGAGGAGGAGACCTACCAGCAGTTCTTGGATTTCTACCATGACGTGCTGCCGGAGTTCAAGAAC
GTGGGAAAGGTGATTCAGTTCAAAGTAAGCTGCAACCTGGAACCTCATCTGCGGGGCAATGTGTATGTTCAGTACCAGTC
GGAAGAAGAATGCCAAGCAGCCCTCTCTCTCTTTAATGGAAGATGGTACGCAGGACGACAGCTCCAGTGTGAATTCTGTC
CAGTGACCCGGTGGAAGGTTGCAATTTGTGGTTTATTCGAAATGCAAAAGTGTCCAAAAGGAAAGCACTGCAACTTCCTT
CATGTGTTCAGAAATCCCAACAACGAATTTAGAGAAGCTAACAGAGACATCTACATGTCTCCTCCGGCTTGGACTGGCTC
CTCTGGTAAAAACTCAGACAGGAGGGAAAGGAAGGACCATCATGAGGAATACTATAGCAAGTCAAGAAGCTACCACTCTG
GTTCATACCACTCCTCCAAGAGAAACAGGGAGTCCGAGAGGAAGAGTCCTCACAGGTGGAAGAAATCTCACAAACAGACA
ACGAAGAGTCATGAGAGGCACAGTTCAAGAAGAGGAAGAGAAGAGGACAGCAGTCCAGGTCCACAAAGCCAGAGCCACAG
AACCTGA

Alignment

ORF - retro_mmus_233 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.73 %
• Parental protein coverage: 80.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TAGPQKLSRKKYLALRKKERRKRRRQALARLREAELAQKEEEEDPLAEEKRLEEERLLEEERQRLHEEWL
          TA.P.KLSRK.Y.A..KKE.RK.RRQ..ARLR..E.A..EE..D..A.E...E..RLLE.ERQRLHEEWL
Retrocopy TAIPEKLSRKQYKAAMKKEKRKKRRQKMARLRALE-APPEEDDDVSANEELAE--RLLEIERQRLHEEWL

Parental  LREEKAQEEFRAKKKKEEEARKRKEELERKLKAEWEEQQRKEREEEEQKRQEKREREEAVQKMLDQAENE
          LREEKAQEEFR.KKKKEE.ARK.KEE.ER..KAEWEEQQ.K.REEEEQK.QEKREREEAVQKMLDQA...
Retrocopy LREEKAQEEFRIKKKKEEAARKQKEEQERQIKAEWEEQQKKQREEEEQKLQEKREREEAVQKMLDQA---

Parental  LENGGTWQNPEPPMDIRVLEKDRANCPFYSKTGACRFGDRCSRKHNFPTSSPTLLIKGMFTTFGMEQCRR
          .EN...WQNPEPP.D.R.LEK.R..CPFY.KTGACRFG.RCSRKH.FPTSSPTLL.K.MFTTFGMEQCRR
Retrocopy -ENERIWQNPEPPKDLR-LEKYRPSCPFYNKTGACRFGNRCSRKHDFPTSSPTLLVKSMFTTFGMEQCRR

Parental  DDYDPDSSLEFSEEEIYQQFLDFYYDVLPEFKSVGKVIQFKVSCNLEPHLRGNVYVQYQSEEDCQAAFSV
          DDYD.D..LE.SEEE.YQQFLDFY.DVLPEFK.VGKVIQFKVSCNLEPHLRGNVYVQYQSEE.CQAA.S.
Retrocopy DDYDSDANLEYSEEETYQQFLDFYHDVLPEFKNVGKVIQFKVSCNLEPHLRGNVYVQYQSEEECQAALSL

Parental  FNGRWYAGRQLQCEFCPVTRWKMAICGLFEVQQCPRGKHCNFLHVFRNPNNEYRDANRDLYPSPDWTSSS
          FNGRWYAGRQLQCEFCPVTRWK.AICGLFE.Q.CP.GKHCNFLHVFRNPNNE.R.ANRD.Y.SP.....S
Retrocopy FNGRWYAGRQLQCEFCPVTRWKVAICGLFEMQKCPKGKHCNFLHVFRNPNNEFREANRDIYMSPPAWTGS

Parental  FGKNSERRERASHYDEYYGRSRRRRRSPSPDFYKRNGESDRKSSSRHRVKKSHRYGMKSRERRSSPSRRR
          .GKNS.RRER..H..EYY..S.R...S.S....KRN.ES.RKS...HR.KKSH....KS.ER.SS...R.
Retrocopy SGKNSDRRERKDHHEEYYSKS-RSYHSGSYHSSKRNRESERKSP--HRWKKSHKQTTKSHERHSSRRGRE

Parental  KDHSPGPWSQSRRS
          .D.SPGP.SQS.R.
Retrocopy EDSSPGPQSQSHRT

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	46.68 RPM	35.39 RPM
SRP007412_cerebellum	84.24 RPM	34.09 RPM
SRP007412_heart	18.09 RPM	13.54 RPM
SRP007412_kidney	29.45 RPM	25.12 RPM
SRP007412_liver	22.07 RPM	9.59 RPM
SRP007412_testis	7.91 RPM	6.63 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_233 in 4 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	11:22971831..22973134
ENCFF001YIJ	POLR2A	11:22972725..22973448
ENCFF001YJZ	POLR2A	11:22971653..22974036
ENCFF001YKA	POLR2A	11:22971681..22973971

EST

6 EST(s) were mapped to retro_mmus_233 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AV574470	22973453	22973954	99.6	498	2	495
BB618009	22973218	22973870	99.4	646	4	642
BE656540	22973567	22973964	100	397	0	397
BI409173	22973195	22973425	98.3	230	0	229
BP776891	22973203	22973425	99.6	221	1	220
BY643991	22973205	22973485	97.2	275	3	271

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_11571	78 libraries	143 libraries	694 libraries	118 libraries	39 libraries
TSS #2	TSS_11572	127 libraries	182 libraries	674 libraries	69 libraries	20 libraries
TSS #3	TSS_11573	719 libraries	304 libraries	38 libraries	6 libraries	5 libraries

The graphical summary, for retro_mmus_233 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_233 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_233 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_176

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009333	1 retrocopy	retro_fcat_44,
Homo sapiens	ENSG00000169249	1 retrocopy	retro_hsap_39,
Gorilla gorilla	ENSGGOG00000011962	1 retrocopy	retro_ggor_1422,
Macaca mulatta	ENSMMUG00000014054	1 retrocopy	retro_mmul_2030,
Mus musculus	ENSMUSG00000031370	1 retrocopy	retro_mmus_233 ,
Mus musculus	ENSMUSG00000061613	3 retrocopies	retro_mmus_1602, retro_mmus_1787, retro_mmus_2955,
Mus musculus	ENSMUSG00000078765	1 retrocopy	retro_mmus_540,
Nomascus leucogenys	ENSNLEG00000009496	1 retrocopy	retro_nleu_1,
Pan troglodytes	ENSPTRG00000021693	1 retrocopy	retro_ptro_25,
Rattus norvegicus	ENSRNOG00000033176	1 retrocopy	retro_rnor_176,
Tarsius syrichta	ENSTSYG00000005278	1 retrocopy	retro_tsyr_1826,