RetrogeneDB ID: retro_rnor_1267

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:44887359..44890203(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ap2b1
• Ensembl ID: ENSRNOG00000009988
• Aliases: None
• Description: AP-2 complex subunit beta [Source:UniProtKB/Swiss-Prot;Acc:P62944]

Sequence

>retro_rnor_1267
ATGACTGACTCCAAGTACTTCACAACCAATAAGAAGGGAGAAATCTTTGAATTAAAAGCTGAACTCAACAATGAAAAGAA
AGAAAAGAGGAAGAAGGCTGTGAAGAGAGTGATTGCTATGATTGTGGGGAAGGATCTGAGCTCTCTCTTCCCAGATGTGG
TGAACTTTATGCAGACTGACAACCTGGACCTAAAGAAGCTTGTGTACCTCTATCTGATGAACTATGCCAAGGGTCAGTCA
GACATGGCCATCATAGCTGTTAACAGCTTTGTGAAGGATTGTGAAGATCCCAATCCTTTGATTTGAGCCTTGGGAGTTAG
AACCATGGGATGCATCCGGGTGGACAAGATTACAGAGTATCTCTGTGAACCCCTCTGCAAGTGCTTGAAGGATGAAGACC
CCTATGTTCAGAAAACAGCAGCAGTATGCGTGGCAAAACTCCATGATATCAATGCCCAGATGGTGGAAGATCAGGGACTT
CTGGATTCTCTGCGGGATCTCATAGCAGATTCAAACCCAATGGTTGTGGCTAATGCTGTAGCAGCATTGTCTGAGATCAG
TGAGTCTCACCCAAACAGCAACTTACTTGATGTGAACCCTCAGAATATCAATAAGCTGCTCACAGCCCTGAATGAGTGCA
CCGAGTGGGGCCAGATTTTCATCTTGGACTGCCTGTCTAATTACAACCCTATAGATGACCGGGAAGCTCAGAGCATCTGT
GAGCGAGTGACGCCTCGCCTCTCTCATGCCAATTCTGCAGTGGTGCTTTCAGCAGTAAAAGTTCTAATGAAGTTTCTAGA
ATGGTTTCCCAAGGATCTGACTACTACAATATGCTGCTAAAGAAGTTAGCGCCTCCACTTGTCACTGTGCTCTCTGGGGA
GCCAGAAGTGCAGTATGTTGCCCTGAGGAACATCAACCTAATTGTCCAGAAAAGGCCTGAAATCTTGAAGCAGGAAATCA
AGGTCTTCTTTGTGAAGTACAATGATCCTATCTATATTAAACTAGAGAAGTTAGACATCATGATTCGTCTTTCATCCCAA
GCCAACATTGCTCAGGTTCTGGCAGAACTGAAGGAATATGCCCTGAAGTTGATGTGGACTTTGTTCGCAAAGCTGTGAGG
GCCATTGGACAGTGTGCCATCAAAGTGGAGCAGACAGCAGAACGCTGTGTAAGCACACTGCTTGATCTAATCCAGACCAA
AGTAAATTATGTGGTTCAAGAGGCAATTGTGGTCATCAGGGACATCTTCCGAAAATACCCCAACAAGTATGAGAGCATTA
TCGCCACGCTGTGTGAGAACTTGGACTCCTTGGATGAACCCGATGCCCGAGCGGCTATGATTTGGATTGTAGGAGAGTAT
GCTGAAAGAATTGATAACACCGATGAGTTACTAGAGAGCTTCCTGGAAGGTTTTCACGATGACAGCACCCAGGTGCAGCT
CACGCTGCTTACCGCCATAGTGAAACTGTTTCTCAAGAAGCCATCAGGAACACAGGAGCTGGTCCAACAGGTCTTGAGCT
TGACCACACAGGATTCTGATAATCCTGACCTTCGAGATCGGGGTTATATTTATTGGCGCCTTCTTTCAACTGACCCTGTG
ACAGCCAAAGAAGTAGTGTTGTCTGAGAAGCCATTGATCTCTGAGGAAACAGACCTCATTGAACCTACCCTCCTGGATGA
GCTCATCTGCCATATTGGTTCTTTGGCCTCCGTGTACCATAAACCTCCAAATGGTTTTGTGGAAGGGAGCCATGGCATTC
ATCGCAAACACTTGCCAATTCACCATGGGAGCACTGATGCGGGTGATAGCCCTGTTGGCACCACCACTGCAACCAACCTG
GAACAGCCTCAGGTCATCCCCTCTCAAGGTGACCTTCTGGGGGATCTTTTAAATCTTGACCTGGGTCCCCCAGTGAATGT
CCTGCAAGTGTCCTCCATGCAGATGGGAGCAATGGATCTTTTAGGAGGACGACTGGATAGCCTGCTTGGCAGTGACCTTG
GCGGGGGCATTGGAGGAAGTCCGGCAGTAGGACAGTCCTTCATCCCGTCATCAGTGCCTGCAACCTTCGCTCCTTCACCT
ACTCCTGCTGTGGTCAGCAGTGGTCTGAATGACCTGTTTGAGCTTTCCACTGGGATAAGCATGGTACCTGGCAGACATGT
GGCTCCTACGGCGGTCTGGCTACCTGCTCTTAAGGCTAAAGGCTTGGAGATTTCGGGGACGTTTACTCACCTCCAAGGGC
ACATCTATATGGAAATGAACTTCACCAACAAAGCCCTGCAGCACATGACGGATTTTGCCATCCAGTTTAACAAGAATAGC
TTCGGTGTCATCCTGAGCACTCCCTTGGCCATACATACTCCACTGATGTCAAACCAGAGCATTGATGTGTCTCTGCCTCT
CAACACCTTGGGCCCATGAAGATGGAACCTCTGAATAACTTGCAGGTGTCTGTTAAAAACAATATTGATGTCTTCTACTT
CAGCTGCCTCATCCCACTCAATGTGCTTTTTGTAGAAAATGGCAAAATGGAACGCCAGGTCTTCCTTGCGATGTGGAAGG
ATATTCCCAATGAAAATGAGTTCCAATTTCAGATTAAGGAGTGTCATTTAAATGCTGACACAGTTTCCAGCAAGTTGCAA
AACGACAGTGTTTACACTATCGCCAGGAGGAATGTGGAAGGGCGGGACATGCTGTACCAGTCCCTGAAGCTCACTAATGG
CATTTGGATTTTGGCAGAGCTGCGGATCCAGCCAGGAAACCCCAATTATACGCTGTTGCTCAAGTGTAGAGCCCCTGAAG
TCTCTCAGTACATCTATCAGGTCTACGACAGCATTTTGAAAAAC

Alignment

ORF - retro_rnor_1267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVY
          MTDSKYFTTNKKGEIFELKAELNNEKKEKRK.AVK.VIA.M.VGKD.SSLFPDVVN.MQTDNL.LKKLVY
Retrocopy MTDSKYFTTNKKGEIFELKAELNNEKKEKRKKAVKRVIA-MIVGKDLSSLFPDVVNFMQTDNLDLKKLVY

Parental  LYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT
          LYLMNYAK.Q.DMAI.AVNSFVKDCEDPNPLI.AL.VRTMGCIRVDKITEYLCEPL.KCLKDEDPYV.KT
Retrocopy LYLMNYAKGQSDMAIIAVNSFVKDCEDPNPLI*ALGVRTMGCIRVDKITEYLCEPLCKCLKDEDPYVQKT

Parental  AAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTA
          AAVCVAKLHDINAQMVEDQG.LDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLD.NPQNINKLLTA
Retrocopy AAVCVAKLHDINAQMVEDQGLLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDVNPQNINKLLTA

Parental  LNECTEWGQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKD-SDYYNM
          LNECTEWGQIFILDCLSNYNP.DDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLE..PKD.SDYYNM
Retrocopy LNECTEWGQIFILDCLSNYNPIDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLEWFPKD<SDYYNM

Parental  LLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQA
          LLKKLAPPLVT.LSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIY.KLEKLDIMIRL.SQA
Retrocopy LLKKLAPPLVTVLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYIKLEKLDIMIRLSSQA

Parental  NIAQVLAELKEYAT-EVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIF
          NIAQVLAELKEYA..EVDVDFVRKAVRAIG.CAIKVEQ.AERCVSTLLDLIQTKVNYVVQEAIVVIRDIF
Retrocopy NIAQVLAELKEYAL<EVDVDFVRKAVRAIGQCAIKVEQTAERCVSTLLDLIQTKVNYVVQEAIVVIRDIF

Parental  RKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAI
          RKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDN.DELLESFLEGFHD.STQVQLTLLTAI
Retrocopy RKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNTDELLESFLEGFHDDSTQVQLTLLTAI

Parental  VKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPT
          VKLFLKKPS.TQELVQQVLSL.TQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPT
Retrocopy VKLFLKKPSGTQELVQQVLSLTTQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPT

Parental  LLDELICHIGSLASVYHKPPNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLL
          LLDELICHIGSLASVYHKPPN.FVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLL
Retrocopy LLDELICHIGSLASVYHKPPNGFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLL

Parental  GDLLNLDLGPPVNVPQVSSMQMGAVDLLGGGLDSLLGSDLGGGIGGSPAVGQSFIPSSVPATFAPSPTPA
          GDLLNLDLGPPVNV.QVSSMQMGA.DLLGG.LDSLLGSDLGGGIGGSPAVGQSFIPSSVPATFAPSPTPA
Retrocopy GDLLNLDLGPPVNVLQVSSMQMGAMDLLGGRLDSLLGSDLGGGIGGSPAVGQSFIPSSVPATFAPSPTPA

Parental  VVSSGLNDLFELSTGIGMAPGGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFA
          VVSSGLNDLFELSTGI.M.PG..VAP.AVWLPA.KAKGLEISGTFTH.QGHIYMEMNFTNKALQHMTDFA
Retrocopy VVSSGLNDLFELSTGISMVPGRHVAPTAVWLPALKAKGLEISGTFTHLQGHIYMEMNFTNKALQHMTDFA

Parental  IQFNKNSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTL-GPVMKMEPLNNLQVAVKNNIDVFYFSCLIPLN
          IQFNKNSFGVI.STPLAIHTPLM.NQSIDVSLPLNTL.GP.MKMEPLNNLQV.VKNNIDVFYFSCLIPLN
Retrocopy IQFNKNSFGVILSTPLAIHTPLMSNQSIDVSLPLNTL<GP-MKMEPLNNLQVSVKNNIDVFYFSCLIPLN

Parental  VLFVEDGKMERQVFLATWKDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKL
          VLFVE.GKMERQVFLA.WKDIPNENE.QFQIKECHLNADTVSSKLQN..VYTIA.RNVEG.DMLYQSLKL
Retrocopy VLFVENGKMERQVFLAMWKDIPNENEFQFQIKECHLNADTVSSKLQNDSVYTIARRNVEGRDMLYQSLKL

Parental  TNGIWILAELRIQPGNPNYTLSLKCRAPEVSQYIYQVYDSILKN
          TNGIWILAELRIQPGNPNYTL.LKCRAPEVSQYIYQVYDSILKN
Retrocopy TNGIWILAELRIQPGNPNYTLLLKCRAPEVSQYIYQVYDSILKN

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
SRP017611_brain	0.07 RPM	102.60 RPM
SRP017611_kidney	0.00 RPM	45.50 RPM
SRP017611_liver	0.07 RPM	13.92 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1267 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1267 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1267 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014853	1 retrocopy	retro_cjac_1850,
Loxodonta africana	ENSLAFG00000015777	1 retrocopy	retro_lafr_446,
Myotis lucifugus	ENSMLUG00000002837	1 retrocopy	retro_mluc_2443,
Mus musculus	ENSMUSG00000035152	1 retrocopy	retro_mmus_2503,
Nomascus leucogenys	ENSNLEG00000013939	2 retrocopies	retro_nleu_1925, retro_nleu_2554,
Pongo abelii	ENSPPYG00000008188	1 retrocopy	retro_pabe_3793,
Pan troglodytes	ENSPTRG00000009021	1 retrocopy	retro_ptro_3248,
Rattus norvegicus	ENSRNOG00000009988	2 retrocopies	retro_rnor_1267 , retro_rnor_574,