RetrogeneDB ID: retro_mmus_2150

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:37077740..37078351(+)
• Located in intron of: ENSMUSG00000027719

Retrocopy information

• Ensembl ID: ENSMUSG00000081705
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zcchc17
• Ensembl ID: ENSMUSG00000028772
• Aliases: Zcchc17, 2810055E05Rik, HSPC251, LDC4, pNO40, pS1D
• Description: zinc finger, CCHC domain containing 17 [Source:MGI Symbol;Acc:MGI:1919955]

Sequence

>retro_mmus_2150
ATCAAAATCCCAGGCTGTAGGAAGCAAGGTCTGGTTCATCGAACTCCCATGTCGTCCTGTCGAGTGGATAAGCCTTCTGC
AATAGTGGATGTTGGAGACAAAGTGTGGGTGAAGCTTATTGGCTGAGAGATGAAAAATGATAGAATAAAAGTGTCCCTCT
CCATGAAAGTTGTCAACTAAGGTACTGGGAAAGACCTCAACAACAACATTGTCATTGAGCAAGAAGAGAGGCACAGTCAG
TCCTTCAGGATTACACTGGGCAGAAGATCACCCTTGAGGCCGTCCTGAACACAACCTGCAAGAAGTGTGGCTGCAAAGGC
CACTTTGCAAAGGACTGTTTCATGCAGCCAGGTGGAACCGAGTATTCTCTGACCCCTGAAGAGGAAGAGGAAAAAGAGGA
GACAAAGGCAAAAGGACTTGAGAAGCCTGATCCCACAAAGAATTCGTCCAGGAAGAGAAAGAAGGAAAAGAAAAAAAAGA
AACATAGAGACAGGAGGTCATCTGATTGTGAAAGCTCTGACTCTGAGAGTGACACGGGCAAGAAGATGAGGCATTCATCA
AAAGACAGCAAGGCCACCAAGAAGAAAAAGAAGAAGCAGCAGCACAAGGAA

Alignment

ORF - retro_mmus_2150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.95 %
• Parental protein coverage: 85.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVNQGTGKDLDPNN
          IKIPGCRKQGLVHRT.MSSCRVDKPS.IVDVGDKVWVKLIG.EMKNDRIKVSLSMKVVN.GTGKDL..NN
Retrocopy IKIPGCRKQGLVHRTPMSSCRVDKPSAIVDVGDKVWVKLIG*EMKNDRIKVSLSMKVVN*GTGKDLN-NN

Parental  VVIEQEERRRRSF-QDYTGQKITLEAVLNTTCKKCGCKGHFAKDCFMQPGGTKYSLIPEEEEEKEEAKAE
          .VIEQEER...SF.QDYTGQKITLEAVLNTTCKKCGCKGHFAKDCFMQPGGT.YSL.PEEEEEKEE.KA.
Retrocopy IVIEQEERHSQSF<QDYTGQKITLEAVLNTTCKKCGCKGHFAKDCFMQPGGTEYSLTPEEEEEKEETKAK

Parental  GLEKPDPTKNSSRKRKKEKKKKKHRDRKSSDCDSSDSESDTGKKARHSSKDSKATKKKKKKKKHKK
          GLEKPDPTKNSS..........KHRDR.SSDC.SSDSESDTGKK.RHSSKDSKATKKKKKK..HK.
Retrocopy GLEKPDPTKNSSXXXXXXXXXXKHRDRRSSDCESSDSESDTGKKMRHSSKDSKATKKKKKKQQHKE

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	0.00 RPM	39.97 RPM
SRP007412_cerebellum	0.00 RPM	42.68 RPM
SRP007412_heart	0.00 RPM	19.11 RPM
SRP007412_kidney	0.00 RPM	20.52 RPM
SRP007412_liver	0.00 RPM	13.03 RPM
SRP007412_testis	0.14 RPM	10.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2150 was not detected

EST

No EST(s) were mapped for retro_mmus_2150 retrocopy.

TSS

No TSS is located nearby retro_mmus_2150 retrocopy 5' end.

Lab

retro_mmus_2150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2150 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017710	1 retrocopy	retro_amel_1501,
Bos taurus	ENSBTAG00000016818	2 retrocopies	retro_btau_168, retro_btau_273,
Canis familiaris	ENSCAFG00000011131	2 retrocopies	retro_cfam_485, retro_cfam_835,
Callithrix jacchus	ENSCJAG00000006259	1 retrocopy	retro_cjac_4218,
Dasypus novemcinctus	ENSDNOG00000000509	1 retrocopy	retro_dnov_2548,
Echinops telfairi	ENSETEG00000007421	1 retrocopy	retro_etel_1280,
Myotis lucifugus	ENSMLUG00000000594	1 retrocopy	retro_mluc_2176,
Monodelphis domestica	ENSMODG00000017082	1 retrocopy	retro_mdom_252,
Mustela putorius furo	ENSMPUG00000015442	1 retrocopy	retro_mputfur_680,
Mus musculus	ENSMUSG00000028772	1 retrocopy	retro_mmus_2150 ,
Sorex araneus	ENSSARG00000007944	1 retrocopy	retro_sara_691,
Tursiops truncatus	ENSTTRG00000014870	2 retrocopies	retro_ttru_1383, retro_ttru_1613,