RetrogeneDB ID: retro_rnor_574

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:38348366..38350957(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000017678
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_574
CTGATGAACTATGCCAAGAGTCAGCCAGACATGGCCATCATGGCTGTCAACAGCTTTGTGAAGGATTGTGAAGATCCCAA
TCCTTTGATTCGAGCCTTGGCAGTTAGAACCATGGGATGCATCCGGGTGGACAAGATTACAGAGTATCTCTGTGAACCCC
TCTGCAAGTGCTTGAAGGATGAAGACCCCTATGTTCGGAAAACAGCAGCAGTATGCGTGGCAAAACTCCATGATATCAAT
GCCCAGATGGTGGAAGATCAGGGATTTCTGGATTCTCTGCGGGATCTCATAGCAGATTCAAACCCAATGGTGGTGGCTAA
TGCTGTAGCAGCATTGTCTGAGATCAGTGAGTCTCACCTAAACAGCAACTTACTTGATCTGAACCCTCAGAATATCAATA
AGCTGCTCACAGCCCTGAATGAGTGCACTGAGTGGGGCCAGATTTTCATCTTGGACTGCCTGTCTAATTACAACCCTAAA
GATGACCGGGAAGCTCAGAGCATCTGTGAGCGAGTGACGCCTCGGCTCTCTTATGCCAATTCTGCAGTGGTGCTTTCAGC
AGTAAAAGTTCTGATGAAGTTTCTAGAGTTGTTACCCAAGGACTCTGACTACTACAATATGCTGCTAAATAAGCTAGCGC
TTCCACTTGTCACTTTGCTCTCTGGGGAGCCAGAAGTGCAGTATGTTGCCCTGAGGAACATCAACCTAATTGTCCAGAAA
AGGCCTGAAAGCTTGAAGCAGGAAATCAAGGTCTTCTTTGTGAAGTACAATGATCCTATCTATGTTAAACTAGAGAAGTT
AGACATCATGATTCGTCTTGCATCCCAAGCCAACATTGCTCAGGTTCTGGCAGAACTGAAAGAATATGCCACTGAAGTTG
ATGTGGACTTTGTTCGCAAAGCTGTGAGGGCCATTGGACGGTGTGCCATCAAAGTGGAGCAGACAGCAGAACGCTGTGTA
AGCACACTGCTCGATCTAATCCAGACCAAAGTAAATTATGTGGTCCAAGAGGCAATTGTTGTCATCAGGGACATCTTCCG
AAAATACCCCAACAAGTATGAGAGCATTATCGCCACGCTGTGTGAGAACTTGGACTCCCTGGCTGAACCCGATGCCCAAG
CGGCTATGATTTGGATTGTAGGAGGGTATGCTGAAAGAATCAATAATGCCGATGAGTTACTAGAGAGCTTCCTGGAAGGT
TTTCATGATGAAAGCACCCAGGTGCAGCTCACGCTGCTTACCGCCATAGTGAAACTGTTTCTCAAGAAGCCATCAGAAAC
ACAGGAGCTGGTCCAACAGGTCTTGAGCTTGGCCACACAGGATTCTGATAATCCTGACCTTCGAGATCGGGGTTATATTT
ATTGGCGCCTTCTTTCAACTGACCCTGTGACAGCCAAAGAAGTAGTGTTGTCTGAGAAGCCATTGATCTCTGAGGAAACA
GACCTCATTGAACCTACCCTCCTGGATGAGCTCATCTGCCACATTGGTTCTTTGGCCTCCGTGTACCATAAACCTCCGAA
TGCTTTTGTGGAAGGGAGCCATGGCCTTCATCGCAAACACTTGCCAATTCACCATGGGAGCACTGATGCAGGTGATAGCC
CTGTTGGCACCACCACTGCAACCAACCTGGAAGAGCCTCAGGTCATCCCCTCTCAAGGTGACCTTCTGGGGGATCTTTTA
AATCTTGACCTGGGTCCCCCAGTGAATGTCCCGCAAGTGTCCTCCATGCAGATGGGAGCAGTGGATCTTTTAGGAGGAGG
ACTGGATAGCCTGGTAGGACAGTCCTTCATCCCGTCATCAGTGCCTGCAACCTTCGCTCCTTCACCTACTCCTGCTGTGG
TCAGCAGTGGTCTGAATGACCTGTTTGAGCTTTCCACTGGGATAGGCATGGCACCTGGCGGATATGTGGCTCCTAAGGCA
GTCTGGCTACCTGCTGTAAAGGCTAAAGGCTTGGAGATTTCGGGGACGTTTACTCACCGCCAAGGGCACATCTATATGGA
AATGAACTTCACCAACAAAGCCCTGCAGCACATGACAGATTTTGCCATCCAGTTTAACAAGAATAGCTTCGGTGTCATCC
CAAGCACTCCCTTGGCCATACATACTCCACTGATGTCAAACCAGAGCATTGATGTGTCTCTGCCTCTCAACACCTTGGGC
CCATGAAGATGGAACCTCTGAATAACTTGCAGGTGGCTGTTAAAAACAATATTGATGTCTTCTACTTCAGCTGCCTCATC
CCACTCAATGTGCTTTTTGTAGAAGATGGCAAAATGGAACGCCAGGTCTTCCTTGCGACGTGGAAGGATATTCCCAATGA
AAATGAGCTCCAATTTCAGATTAAGGAGTGTCATTTAAACGCTGACACAGTTTCCAGCAAGTTGCAAAACAACAATGTTT
ACACTATCGCCAAGAGGAATGTGGAGGGGCAGGACATGCTGTACCAGTCCCTGAAGCTCACTAATGGCATTTGGATTTTG
GCAGAGCTGCGGATCCAGCCAGGAAACCCCAATTATACGCTGTCGCTGAAGTGTAGAGCCCCTGAAGTCTCTCAGTACAT
CTATCAGGTCTACGACAGCATTTTGAAAAAC

Alignment

ORF - retro_rnor_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.15 %
• Parental protein coverage: 92.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAA
          LMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPL.KCLKDEDPYVRKTAA
Retrocopy LMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLCKCLKDEDPYVRKTAA

Parental  VCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTALN
          VCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESH.NSNLLDLNPQNINKLLTALN
Retrocopy VCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHLNSNLLDLNPQNINKLLTALN

Parental  ECTEWGQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLK
          ECTEWGQIFILDCLSNYNPKDDREAQSICERVTPRLS.ANSAVVLSAVKVLMKFLELLPKDSDYYNMLL.
Retrocopy ECTEWGQIFILDCLSNYNPKDDREAQSICERVTPRLSYANSAVVLSAVKVLMKFLELLPKDSDYYNMLLN

Parental  KLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIA
          KLA.PLVTLLSGEPEVQYVALRNINLIVQKRPE.LKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIA
Retrocopy KLALPLVTLLSGEPEVQYVALRNINLIVQKRPESLKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIA

Parental  QVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRKYP
          QVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQ.AERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRKYP
Retrocopy QVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQTAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRKYP

Parental  NKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIVKLF
          NKYESIIATLCENLDSL.EPDA.AAMIWIVG.YAERI.NADELLESFLEGFHDESTQVQLTLLTAIVKLF
Retrocopy NKYESIIATLCENLDSLAEPDAQAAMIWIVGGYAERINNADELLESFLEGFHDESTQVQLTLLTAIVKLF

Parental  LKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPTLLDE
          LKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPTLLDE
Retrocopy LKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPTLLDE

Parental  LICHIGSLASVYHKPPNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLLGDLL
          LICHIGSLASVYHKPPNAFVEGSHG.HRKHLPIHHGSTDAGDSPVGTTTATNLE.PQVIPSQGDLLGDLL
Retrocopy LICHIGSLASVYHKPPNAFVEGSHGLHRKHLPIHHGSTDAGDSPVGTTTATNLEEPQVIPSQGDLLGDLL

Parental  NLDLGPPVNVPQVSSMQMGAVDLLGGGLDSLVGQSFIPSSVPATFAPSPTPAVVSSGLNDLFELSTGIGM
          NLDLGPPVNVPQVSSMQMGAVDLLGGGLDSLVGQSFIPSSVPATFAPSPTPAVVSSGLNDLFELSTGIGM
Retrocopy NLDLGPPVNVPQVSSMQMGAVDLLGGGLDSLVGQSFIPSSVPATFAPSPTPAVVSSGLNDLFELSTGIGM

Parental  APGGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAI
          APGGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAI
Retrocopy APGGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAI

Parental  HTPLMPNQSIDVSLPLNTL-GPVMKMEPLNNLQVAVKNNIDVFYFSCLIPLNVLFVEDGKMERQVFLATW
          HTPLM.NQSIDVSLPLNTL.GP.MKMEPLNNLQVAVKNNIDVFYFSCLIPLNVLFVEDGKMERQVFLATW
Retrocopy HTPLMSNQSIDVSLPLNTL<GP-MKMEPLNNLQVAVKNNIDVFYFSCLIPLNVLFVEDGKMERQVFLATW

Parental  KDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWILAELRIQPGNPN
          KDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWILAELRIQPGNPN
Retrocopy KDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWILAELRIQPGNPN

Parental  YTLSLKCRAPEVSQYIYQVYDSILKN
          YTLSLKCRAPEVSQYIYQVYDSILKN
Retrocopy YTLSLKCRAPEVSQYIYQVYDSILKN

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	0.50 RPM	102.60 RPM
SRP017611_kidney	0.42 RPM	45.50 RPM
SRP017611_liver	0.20 RPM	13.92 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_574 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_574 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 ,