RetrogeneDB ID: retro_mmus_3726

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:163760239..163760974(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083695
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rnf138
• Ensembl ID: ENSMUSG00000024317
• Aliases: Rnf138, 2410015A17Rik, 2810480D20Rik, STRIN, Trif, Trif-d
• Description: ring finger protein 138 [Source:MGI Symbol;Acc:MGI:1929211]

Sequence

>retro_mmus_3726
GAAGAATCTGCCTCCACCACGTCTTATACTGAAGATGATTTCTACTGTCCGATATGCCAAGAAGTCTTCAAAACGCCAGT
TCGGGTCGCGGCCTGTAAGCATGTTTTCTGCAGAAAATGTTTCCTGAGTGCAATGAAGGAGAGCCGGCTCCACTGCCCCC
TGTGCCGTGGAAATGTGACTAGAAGAGAAAGAGCTTGTCCAGTGAGGGCTGTAGACCTCGAAACCATCATGAGACATTTT
CCTGGTAATTGCCGATGCTGTTCCCAGCGCGTTGAACTCTATCGTATGAGGCAGCACTACAAAACTTGCGAAAAGTACCA
GGATGAATTTGGAGTTTCTACATCTGTTTCAAGCTTCCAACAGTCTCCAAACTCCGTGGGCAACAGTAACAACGAGGCAC
CGGCCTCAGCGAATGCTGAGGTTTTACAAGAAGAGGAAGAGAACGCAAGCCCACCTGATGAGCCCACCTTCGATTGTCCT
CTGTGTGAAGAAGTAACCATGAGCAGGCAACGTTTGCTGGATCATTGCAACAGCAGCCACCGAGGTCGTGTCGTTTCAGT
CACTTGCCCAATTTGCCTATCTCTTCCATGGGGCGACCCGCCTCAACTCACCAGAAATTTTGTTAGTCACCTTAATCAGA
GGCATCAGTTTGATTACGGAGATTTCGTGAATCTTCAGCTGGATGAGGAAACCCAATTTCAGATCGCCATTGAAGAGTCC
TTCCACGTCAACATC

Alignment

ORF - retro_mmus_3726 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.29 %
• Parental protein coverage: 99.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EELSAATSYTEDDFYCPVCQEVLKTPVRTAACQHVFCRKCFLTAMRESGIHCPLCRGSVTRRERACPERA
          EE....TSYTEDDFYCP.CQEV.KTPVR.AAC.HVFCRKCFL.AM.ES..HCPLCRG.VTRRERACP.RA
Retrocopy EESASTTSYTEDDFYCPICQEVFKTPVRVAACKHVFCRKCFLSAMKESRLHCPLCRGNVTRRERACPVRA

Parental  LDLENIMRRFSGSCRCCSKKIKFYRMRHHYKSCKKYQDEYGVSSVIPNFKISQDSVRSSNRSETSASDNT
          .DLE.IMR.F.G.CRCCS.....YRMR.HYK.C.KYQDE.GVS.....F..S..SV..SN..E..AS.N.
Retrocopy VDLETIMRHFPGNCRCCSQRVELYRMRQHYKTCEKYQDEFGVSTSVSSFQQSPNSVGNSN-NEAPASANA

Parental  ETYQEDTSSSGHP---TFKCPLCQESNFTRQRLLDHCNSNHLFQIVPVTCPICVSLPWGDPSQITRNFVS
          E..QE.......P...TF.CPLC.E....RQRLLDHCNS.H....V.VTCPIC.SLPWGDP.Q.TRNFVS
Retrocopy EVLQEEEENASPPDEPTFDCPLCEEVTMSRQRLLDHCNSSHRGRVVSVTCPICLSLPWGDPPQLTRNFVS

Parental  HLNQRHQFDYGEFVNLQLDEETQYQTAVEESFQVNM
          HLNQRHQFDYG.FVNLQLDEETQ.Q.A.EESF.VN.
Retrocopy HLNQRHQFDYGDFVNLQLDEETQFQIAIEESFHVNI

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	0.16 RPM	9.06 RPM
SRP007412_cerebellum	0.35 RPM	4.86 RPM
SRP007412_heart	0.00 RPM	3.18 RPM
SRP007412_kidney	0.00 RPM	6.14 RPM
SRP007412_liver	0.00 RPM	6.31 RPM
SRP007412_testis	11.62 RPM	217.72 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3726 was not detected

EST

No EST(s) were mapped for retro_mmus_3726 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_156229	902 libraries	135 libraries	30 libraries	1 library	4 libraries
TSS #2	TSS_156230	856 libraries	179 libraries	30 libraries	3 libraries	4 libraries

The graphical summary, for retro_mmus_3726 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_3726 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3726 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000009856	1 retrocopy	retro_eeur_430,
Monodelphis domestica	ENSMODG00000010850	4 retrocopies	retro_mdom_1468, retro_mdom_387, retro_mdom_708, retro_mdom_725,
Mus musculus	ENSMUSG00000024317	2 retrocopies	retro_mmus_3726 , retro_mmus_494,
Mus musculus	ENSMUSG00000033107	2 retrocopies	retro_mmus_3069, retro_mmus_513,
Ochotona princeps	ENSOPRG00000011494	1 retrocopy	retro_opri_554,