RetrogeneDB ID: retro_mmus_3623

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:60045113..60046229(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000046993
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Arpc1b
• Ensembl ID: ENSMUSG00000029622
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1B [Source:MGI Symbol;Acc:MGI:1343142]

Sequence

>retro_mmus_3623
ATGGCCTACCACAGCTTCCTGGTGGAGCCCATCAGCTGCCATGCCTGGAACAAGGACCGCACACAGATCGCCATCTGCCC
CAACAACCATGAGGTACACATCTATGAGAAGAGCGGTGCCAAGTGGAACAAGGTGCACGAGCTCAAGGAGCACAACGGGC
AGGTGACAGGCATCGACTGGGCCCCTGAGCATAACCGCATTGTGACCTGTGGCACAGACAGCAATGCCTATGTGTGGACG
CTGAAGGGCCGCACGTGGAAGCCCACACTGGTCATCCTCCGGATCAATCGAGCTGCCCGCTGTGTGCGCTGGGCCCCCAG
TGAGAACAAGTTCGCTGTGGGCAGCGGCTCCCGGGTCATTTCCATCTGTTATTTTGAGCAGGAGAATGACTGGTGGGTGT
GCAAACACATCAAAAAGCCCATCAGCTCCACTGTCCTCAGCCTGGACTGGCATCCCAACAACGTGCTCCTGGCAGCAGGC
TCCTGTGACTTCAAGTGCAGGATCTTCTCTGCCTATATCAAGGAGGTGGAAGAACGGCCAGCCCCTACACCGTGGGGCTC
CAAGATGCCCTTTGGGGAGCTGATGTTTGAATCGAGCAGCAGCTGTGGCTGGGTGCACGGTGTCTGCTTCTCGGCCAGTG
GGAGCCGAGTTGCTTGGGTCAGCCATGACAGCACTGTATGCCTGGTAGATGCTGACAAGAAGATGGCCGTGGCAACCCTG
GCCTCTGAGACATTACCACTCTTGGCCGTCACCTTCATCACAGAAAATAGTCTAGTGGCAGCAGGCCACGACTGCTTCCC
GGTGCTGTTTACCTATGACAATGCTGCGGTGACATTGAGCTTCGGTGGCCGGCTGGATGTTCCCAAGCAGAGCTCCCAGC
GTGGCATGGCAGCCCGAGAGCGCTTCCAGAACCTGGACAAGAAGGCCAGCTCTGAGGGGGGTGCAGCCACTGGGGCTGGC
CTGGATTCACTGCACAAGAACAGCATCAACCAAATCTCGGTGCTCATCGGGGGCAAGGCCAAGTGCTCACAGTTCTGCAC
TACAGGCATGGATGGTGGCATGAGCATCTGGGACGTGAAGAGCCTGGAGTCAGCCTTGAAGAACCTGAAGATCAAA

Alignment

ORF - retro_mmus_3623 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGAKWNKVHELKEHNGQVTGIDWAPESNRIVTC
          MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGAKWNKVHELKEHNGQVTGIDWAPE.NRIVTC
Retrocopy MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGAKWNKVHELKEHNGQVTGIDWAPEHNRIVTC

Parental  GTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNENKFAVGSGSRVISICYFEQENDWWVCKHIKKP
          GTD.NAYVWTLKGRTWKPTLVILRINRAARCVRWAP.ENKFAVGSGSRVISICYFEQENDWWVCKHIKKP
Retrocopy GTDSNAYVWTLKGRTWKPTLVILRINRAARCVRWAPSENKFAVGSGSRVISICYFEQENDWWVCKHIKKP

Parental  IRSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCF
          I.STVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCF
Retrocopy ISSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCF

Parental  SASGSRVAWVSHDSTVCLVDADKKMAVATLASETLPLLAVTFITENSLVAAGHDCFPVLFTYDNAAVTLS
          SASGSRVAWVSHDSTVCLVDADKKMAVATLASETLPLLAVTFITENSLVAAGHDCFPVLFTYDNAAVTLS
Retrocopy SASGSRVAWVSHDSTVCLVDADKKMAVATLASETLPLLAVTFITENSLVAAGHDCFPVLFTYDNAAVTLS

Parental  FGGRLDVPKQSSQRGMTARERFQNLDKKASSEGGAATGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGM
          FGGRLDVPKQSSQRGM.ARERFQNLDKKASSEGGAATGAGLDSLHKNS..QISVL.GGKAKCSQFCTTGM
Retrocopy FGGRLDVPKQSSQRGMAARERFQNLDKKASSEGGAATGAGLDSLHKNSINQISVLIGGKAKCSQFCTTGM

Parental  DGGMSIWDVKSLESALKDLKIK
          DGGMSIWDVKSLESALK.LKIK
Retrocopy DGGMSIWDVKSLESALKNLKIK

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	0.02 RPM	11.10 RPM
SRP007412_cerebellum	0.09 RPM	10.38 RPM
SRP007412_heart	0.19 RPM	50.31 RPM
SRP007412_kidney	0.83 RPM	52.03 RPM
SRP007412_liver	0.30 RPM	39.60 RPM
SRP007412_testis	2.33 RPM	25.02 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3623 was not detected

EST

No EST(s) were mapped for retro_mmus_3623 retrocopy.

TSS

No TSS is located nearby retro_mmus_3623 retrocopy 5' end.

Lab

retro_mmus_3623 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3623 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046248	2 retrocopies	retro_btau_1547, retro_btau_473,
Canis familiaris	ENSCAFG00000015081	1 retrocopy	retro_cfam_1568,
Callithrix jacchus	ENSCJAG00000015849	1 retrocopy	retro_cjac_2365,
Echinops telfairi	ENSETEG00000009924	2 retrocopies	retro_etel_1076, retro_etel_1275,
Gorilla gorilla	ENSGGOG00000013186	2 retrocopies	retro_ggor_1337, retro_ggor_1455,
Microcebus murinus	ENSMICG00000017424	1 retrocopy	retro_mmur_602,
Myotis lucifugus	ENSMLUG00000010933	1 retrocopy	retro_mluc_974,
Mustela putorius furo	ENSMPUG00000016522	1 retrocopy	retro_mputfur_1578,
Mus musculus	ENSMUSG00000029621	1 retrocopy	retro_mmus_1373,
Mus musculus	ENSMUSG00000029622	2 retrocopies	retro_mmus_1340, retro_mmus_3623 ,
Otolemur garnettii	ENSOGAG00000010872	2 retrocopies	retro_ogar_2380, retro_ogar_3087,
Rattus norvegicus	ENSRNOG00000000991	2 retrocopies	retro_rnor_1105, retro_rnor_967,
Sus scrofa	ENSSSCG00000007625	1 retrocopy	retro_sscr_374,