RetrogeneDB ID: retro_mmus_3323

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:26961093..26962559(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Zc3h11a
• Ensembl ID: ENSMUSG00000026464
• Aliases: Zc3h11a, 1110003F06Rik, 5730454B08Rik, G630041M05Rik, Zc3hdc11a, Zc3hh11a, mKIAA0663
• Description: zinc finger CCCH type containing 11A [Source:MGI Symbol;Acc:MGI:1917829]

Sequence

>retro_mmus_3323
ATGCCTAATCAGGGAGAAGACTGCTATTTTTATTTCTATTCTACATGCGCCGAAGGTGACAGCTGCTCATTCCGTCACTG
TGAAGCTGCACTGGGAAATGAAACTGTTTGCACACTATGGCAAGAAGGTCCTTGTTTTCAACAAGTGTGCAGATTTCACC
ACATGGAAGTTGACAAAAAACAAAGTGAAATTCCTTGTTATTGGGAAAATCAGCCATGGTGATGTCAAAAAACTAAACTG
TGCTTTCCATTACACCAGAAGCCACTATGTTGATGGACTCTTCATACCTCCAAGCAAAACTGTGTTACCCACTGTGCCTG
AGTCTCAAGAAGAAGTAAAGATTAGCCAGCTTTACAGTTCAACAGAACAAATTGTTCAGTCTAACCCCTCCCCTCAGCTG
CGGAGTGTAATGAAAGTAGAGAGCTCAGAAAATGTTCCCAGCCCCACACATCCGCCTGTTGTAATCAATGCTGCAGATGA
TAATGAAGATGACCATGATCAGTTTTCTGAGGAAGGTGATGAGAGCAAGACACCTGCCCTGCAACCAACTCCTGACGTCC
ATAATGGATTACGAGTGGCTTCTGCCCGCAAACCTGGAGTCAGTTTAAAGCAAGGTGAATGTTTGAATTTTGGAATAAAG
ACTCTTGAGGAAATTAAATCAAAGAAAATGAAGGAAAAATCCAAGAAGCAAGATAGCTCCTCGGGAGTTTCCAGGGTTTT
ACATCAGCCTCAGTCCAATCCAGGCCCTGAGAGGAGAATGTTTGGGCTGTGATGAGGATGGTAACTCTATCAAGCAAACC
AGAAGAGCCCTTGGTTAGACTGAGTCTTTCTGAGAGACTGGGGAAACGAAAACTTTCAGTAGGTGGTGACAGTGACCCTC
CATTAAAGTGAAGCCTTGCACAGAGACTGGGGAAAAAAGTGGAAGCGCCAGAAACTAACATTGATAAAGCACCAAAGAAA
GAGCGAGGTCATAAAGCTGGGGAGATCCATGTGAAGACACTGGAAGAAATTCTTCTTGAAAGAGCCAGTCAGAAACTGGA
GATTTGCAAACTAAACTGAGGACAGAAGAACCTTCAGGAGCTGATGATTCTCCATCGGGAACAAAAAGTTCTTCTTCAGT
GCGGATCAAAACCTTCTTTGAAGTCCTGTCCGAAAAGAAACATCGGCAGCAGGAAATGGAAAGACAGAAATCCAAAAAGG
ATACAAGTTGCCTCATGCTAACAGAAGACACTGAAGTGAAAAAGACAGTGAGTCTGCCGACTGTTGCTGATAGCAAAGGA
CAACCAGAGGAGTCTGCAGGAAGAGCCAGGTCTAAGCAGGAGGTGCATATTAAGCCACTAGAGGAAATTAAGCTGGAGAA
GGCCCAGAGGGTGCAGCAAAGCTCTGAGAGTAGTGGCAACTCCTGACCTCAAGCTGAGGCTGCCTCAGGGACAAAGAGGC
TGCACGGAATCACCAAGAGAGCAGGT

Alignment

ORF - retro_mmus_3323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.28 %
• Parental protein coverage: 62.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPNQGEDCYFYFYSTCAKGDSCPFRHCEAALGNETVCTLWQEGRCFRQVCRFRHMEIDKKRSEIPCYWEN
          MPNQGEDCYFYFYSTCA.GDSC.FRHCEAALGNETVCTLWQEG.CF.QVCRF.HME.DKK.SEIPCYWEN
Retrocopy MPNQGEDCYFYFYSTCAEGDSCSFRHCEAALGNETVCTLWQEGPCFQQVCRFHHMEVDKKQSEIPCYWEN

Parental  QPVGCQK-LNCAFHHTRSRYVDGLFLPPSKTVLPTVPESQEEEVKTSQLTVQQSKLSVQSNPSPQLRSVM
          QP..CQK.LNCAFH.TRS.YVDGLF.PPSKTVLPTVPESQEE.VK.SQL........VQSNPSPQLRSVM
Retrocopy QPW*CQK>LNCAFHYTRSHYVDGLFIPPSKTVLPTVPESQEE-VKISQLYSSTEQI-VQSNPSPQLRSVM

Parental  KVESSENVPSPTHPPVVINAADDDEDDDDQFSEEGDESKTPALQPSPDVHNGLRVASARKPGVSLKQGEC
          KVESSENVPSPTHPPVVINAADD.EDD.DQFSEEGDESKTPALQP.PDVHNGLRVASARKPGVSLKQGEC
Retrocopy KVESSENVPSPTHPPVVINAADDNEDDHDQFSEEGDESKTPALQPTPDVHNGLRVASARKPGVSLKQGEC

Parental  LNFGIKTLEEIKSKKMKEKSKKQGEGSSGVSSVLQQPQPNPGPEK-ENVRTVVRMVTLSSKPEEPLVRLS
          LNFGIKTLEEIKSKKMKEKSKKQ...SSGVS.VL.QPQ.NPGPE..ENV..V.RMVTLSSKPEEPLVRLS
Retrocopy LNFGIKTLEEIKSKKMKEKSKKQ-DSSSGVSRVLHQPQSNPGPER<ENVWAVMRMVTLSSKPEEPLVRLS

Parental  LSERLGKRKLSVGGDSDPPLKRSLAQRLGKKVESPETNIDKAPKKERGHKAGEIHVKTLEEILLERASQK
          LSERLGKRKLSVGGDSDPPLK.SLAQRLGKKVE.PETNIDKAPKKERGHKAGEIHVKTLEEILLERASQK
Retrocopy LSERLGKRKLSVGGDSDPPLK*SLAQRLGKKVEAPETNIDKAPKKERGHKAGEIHVKTLEEILLERASQK

Parental  -RGELQTKLKAEEPSGADDSPSGTKSSSSVRIKTFSEVLAEKKHRQQEMERQKSKKDTSCLTLTDDTEMK
          ..G.LQTKL..EEPSGADDSPSGTKSSSSVRIKTF.EVL.EKKHRQQEMERQKSKKDTSCL.LT.DTE.K
Retrocopy <TGDLQTKLRTEEPSGADDSPSGTKSSSSVRIKTFFEVLSEKKHRQQEMERQKSKKDTSCLMLTEDTEVK

Parental  KTVSLPTVAVSKGQPEEPAGRARSMQEVHIKTLEEIKLEKALRVQQSSESSGNSRPQAEAAPGTKRLLRI
          KTVSLPTVA.SKGQPEE.AGRARS.QEVHIK.LEEIKLEKA.RVQQSSESSGNS.PQAEAA.GTKRL..I
Retrocopy KTVSLPTVADSKGQPEESAGRARSKQEVHIKPLEEIKLEKAQRVQQSSESSGNS*PQAEAASGTKRLHGI

Parental  TKRAG
          TKRAG
Retrocopy TKRAG

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	0.02 RPM
SRP007412_cerebellum	0.04 RPM	0.04 RPM
SRP007412_heart	0.06 RPM	0.00 RPM
SRP007412_kidney	0.02 RPM	0.02 RPM
SRP007412_liver	0.00 RPM	0.03 RPM
SRP007412_testis	0.09 RPM	0.09 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3323 was not detected

EST

No EST(s) were mapped for retro_mmus_3323 retrocopy.

TSS

No TSS is located nearby retro_mmus_3323 retrocopy 5' end.

Lab

retro_mmus_3323 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3323 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000058673	2 retrocopies	retro_hsap_3481, retro_hsap_508,
Monodelphis domestica	ENSMODG00000001184	1 retrocopy	retro_mdom_1449,
Mus musculus	ENSMUSG00000026464	2 retrocopies	retro_mmus_3323 , retro_mmus_564,
Otolemur garnettii	ENSOGAG00000000243	1 retrocopy	retro_ogar_3250,
Pan troglodytes	ENSPTRG00000001876	5 retrocopies	retro_ptro_2980, retro_ptro_2981, retro_ptro_2991, retro_ptro_380, retro_ptro_382,
Rattus norvegicus	ENSRNOG00000002993	3 retrocopies	retro_rnor_1570, retro_rnor_1673, retro_rnor_602,