RetrogeneDB ID: retro_rnor_2044

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:28122693..28126746(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Golga3
• Ensembl ID: ENSRNOG00000037437
• Aliases: None
• Description: Golgin subfamily A member 3 [Source:RefSeq peptide;Acc:NP_001101317]

Sequence

>retro_rnor_2044
TCTACTGCATCTTCACTGCCCTTGGAAAAGGAGGAGCAGGTCCGACTGCAGGCCCGGAAGCGCCTGGAAGAGCAGCTGAT
GCAATACCGAGTTAAGCGCCATCGGGAAAGGTCCAGTCAGCCGGCAACTAAAATGAAACTTTTTAGTACACTTGATCCTG
AGCTCATGTTAAATCCAGAAAACTTGCCAAGGGCCAGTGCTGTAGCTGTGACAAAAGAATATTCCTTCCTGCGTACCAGT
GTTCCTCGGGGGCCCAAGGTAGGCAGCTTAGGGCTGCTGGCACATTCTAAAGAGAAGAAGAATTCCAAGTCAAGCAAGAT
TCGGTCTCTGGCTGACTATAGAACTGAAGATCCAAGTGACTCTGGTGGCCTTGGTTCTACTGCTGATGCTGTTGGAAGTT
CCCTGAAACAGAGTAGAAGTAGCACTTCAGTTGTGTCTGAAGTGAGCCCATCATGTGAGACTGATAACCGTGCAGAGAGT
GCCTCACTGGCTGGGGACAGTGTGTCAGAGGCTGATGGAAATGAGAGTGACAGTTCCTCACACAGCAGCTTCTCTGCCCG
AGGGGCCTGTGCTGTCCTGGGGAATGTCGGCACACCAGGAGCAGCTTATGTGGTTGATGGCCAGGAGATTTCTGCTGAGG
CCCTGGGCCAGTTTCCTTCGATTAAAGACGTGCTACAGGCTGCAGCAGCCCAGCACCAAGATCAGAACCAGGAAGCCAAT
GGGGAGGTGCAGAGCCGCAGAGACAGCATCTGCAGCAGTGTGTCCATGGAGAGCTCTTTTGCTGAACCACAGGAAGAATT
GTTGCAGATCCTTAAAGATAAGAGGAGACTTGAAGGACAGGTGGAGGCTTTGTCATTAGAAGCCAGTCAGGCACTTCAAG
AGAAGGCTGAGCTACAGGCCCAGCTTGCTGCCCTGAGCACAAGGCTACAGGCACAGGTGGAACACAGTCACAGCAGCCAG
CAGAAGCAAGACTCCCTTAGTTCTGAAGTGGACACTTTGAAGCAGTCTTGCTGGGATTTGGAGCGGGCTATGACTGACCT
GCAGAACATGCTAGAAGCTAAAAATGCCAGCCTGGCATCGTCAAACAATGACCTACAAGTGGCAGAGGAGCAGTATCAGA
GACTGATGGCCAAAGTGGAGGCCATGCAGAGAAACATCCTTAGCAAGGACAACACAGTTCATGACCTGCGGCAGCAGATG
ACAGCGCTACAGAGCCAGCTCCAGCAAGTACAGCTGGAGCGCACAACACTGACCAGCAAACTACAAGCATCACAGGCTGA
AATCACTTCTTTGCAGCAGGCCCGGCAGTGGTACCAACAGCAGCTTGCTTTGGCCCAGGAGGCCAGAGTCAGGCTGCAAG
GAGAGATGGCCCACATCCAGGTCGGACAGATGACTCAAGCGGGCCTTTTGGAGCACCTGAAACTTGAGAATGTGTCCCTA
TCGCATCAGCTAACAGAAACTCAGCACAGATCCATCAAGGAAAAAGAGCGCATAGCTGTTCAGCTCCAGAGCATTGAGGC
TGACATGTTAGATCAGGAGGCAGCATTTGTACAGATTCGGGAGGCGAAGACAATGGTGGAAGAAGACCTCCAAAGGAAGC
TGGAAGAATTTGAAGGTGAACGGGAACAGTTACAGAAAGTGGCGGATGCAGCAGCGTCCCTGGAGCAACAGTTGGAACAG
GTGAAGTTGACATTGTTCCAGCGAGATCAGCAGCTGGCAGCACTTCAGCAGGAGCATCTAGATGTGATAAAGCAGCTTAC
ATCGACACAGGAGGCTCTACAGGCCAAAGGGCAGTCCCTCGATGACCTGCAAACACGTTATGATGAGCTACAAGCAAGGC
TGGAAGAGCTTCAGAGAGAGGCTGACTCCAGGGAGGATGCCATTCACTTCTTGCAGAATGAGAAGATTGTCTTAGAAGTG
GCTCTGCACTCAGCCAGGAGTGACAAGGAGGAACTTGACAGAGGAGCACGGTGTTTGGAAGAAGATACTGAGGAGACATC
AGGACTTTTAGAACAATTGAGACAAGATGTGGCTGTCAAGTCCAACCAGGTGGAACACTTGCAGCAAGAGACAGCCACAT
TGAGAAAACAGATGCAGAAAGTAAAGGAGCAGTTTCTTCAGCAAAAGGTGATGGTAGAGGCCTATCGGCGAGATGCTGCT
TCTAAAGACCAACTCATCAATGAGCTGAAAGCTACCAAAAAACGCCTGGACTCAGAGATGAAGGAACTGAGGCAGGAGCT
GATCAAGCTGCATGGAGAGAAGAAGACTGTGGAAGTAGAGCACTCACGGCTGCAGAAGGACATGTCCCTGGTTCACCAGC
AGATGGCAGAGCTTGAGGGGCATCTCCAGTCGGTGCAGAAAGAGCGAGATGAAATGGAGATTCACCTGCAGTCTTTGAAG
TTTGACAAAGAGCAGATGATAGCCCTTACTGAGGCCAATGAGACACTAAAGAAACAAATAGAGGAGCTGCAGCAAGAGGC
CAAGAAGGCCATCACAGAACAGAAGCAGAAGATGAAGCGGCTGGGCTCAGATCTGACCAGTGCCCAGAAGGAGATGAAGA
CTAAGCACAAGGCTTACGAGAATGCTGTGAGCATTCTCAGCCGTCGCCTACAGGAGGCTCTGGCTAACAAGGAGGCCACA
GATGCGGAGCTGAACCAGCTCAGAGCTCAGAGCACAGGTGGCAGCAGTGACCCTGCTCTACATGAGAAGATTCATGCTCT
GGAGGTGGAACTGCAGAATGTTGGCCAAAGCAAAATACTGCTGGAGAAGGAGTTACAGGAGGTGATCACGATGACTAGCC
AGGAGTTGGAAGAGTCCCGGGAGAAGGTGCTGGAGCTCGAGGATGAGCTTCAAGAATCCAGAGGCTTCAGATGGAAGATA
AAACGTCTTGAAGAGTCAAATAAGAAGCTAGCTCTGGAGTTAGAACATGAGCGAGGGAAGCTCACCGGCCTTGGACAATC
TAATGCGGCTTTGCGGGAGCACAACAGCATTCTGGAAACTGCACTAGCCAAGAGGGAAGCTGACCTGGTGCAGCTGAATC
TCCAGGTGCAGGCAGTTTTACAGCGCAAAGAGGAGGAGGATCGCCAGATGAAGCAACTTGTCCAAGCCTTACAAATCTCA
TTAGAGAAAGAAAAGACGGAAGTGAGCAGCCTGAAGGAACAGATGGCTGCTGCCAGGGTGGAAGCTGGGCACAACCGCCG
CCACTTTAAGGCAGCAACTTTGGAGCTGAGTGAGGTGAAGAAAGAATTGCAGGCCAAAGAACACCTGGTACAGACACTGC
AGGCCGAGGTGGATGAGCTCCAGATTCAGGAGGGAAAGCATTCTCAAGAAATCGCTCAATTCCAGACTGAGCTGGCAGAA
GCTAGGACCCAGCTCCAGCTCCTGCAGAAGAAGCTCGAAGAACAGAGGAGCCAGCAACCAACAGGGAGCCAAGAGATGGA
AGATCTCAAATGGGAATTGGATCAGAAAGAATGAGAGATTCAGTCCCTGAAGCAGCAGCTTGACTTGACAGAGCACCAGG
GCAAGAAAGAACTCGAGGGTACACAACAGACACTGCAGACTATCAAGTCTGAGTTGGAAACGGTTCAGGAAGATCTGTCT
GAGACCCAGAAGGATAAGTTTATGCTTCAAGCCAAAGTGTCTGAACTGAAGAACAACATGAAGACTCTGCTGCAGCAGAA
CCAACAGCTCAAGCTGGATCTCCGCCGCGGTGCAGCCAAGAAGAAAGAGCCAAAAGGTGAGTCCAGCTCATCCAGTCCAG
CAACACCCATCAAGATACCAGACTGCCCTGTCCCAGCCTCACTGCTGGAGGAGCTGCTGAGGCCCCCACCCGCTGTGAGC
AAGGAGCCCCTGAAGAATCTCAACAGCTGTTTGCAGCAGCTCAAGCAGGAAATGGACAGTCTACAGCGCCAGATGGAGGA
GCATACCATCACTGTGCATGAGTCCCTGTCCTCGTGGGCTCAGGTGGAAGCTGCCCCAGCAGAGCATGCCCATGCCCGGG
GAGACACAAAAGTACACAATCAAAACAGTGTTCCTGGAGAAGGGCTGGGCCAA

Alignment

ORF - retro_rnor_2044 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.78 %
• Parental protein coverage: 93.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STASSLPLEKEEQVRLQARKRLEEQLMQYRVKRHRERSSQPATKMKLFSTLDPELMLNPENLPRASAVAV
          STASSLPLEKEEQVRLQARKRLEEQLMQYRVKRHRERSSQPATKMKLFSTLDPELMLNPENLPRASAVAV
Retrocopy STASSLPLEKEEQVRLQARKRLEEQLMQYRVKRHRERSSQPATKMKLFSTLDPELMLNPENLPRASAVAV

Parental  TKEYSFLRTSVPRGPKVGSLGLLAHSKEKKNSKSSKIRSLADYRTEDPSDSGGLGSTADAVGSSLKQSRS
          TKEYSFLRTSVPRGPKVGSLGLLAHSKEKKNSKSSKIRSLADYRTEDPSDSGGLGSTADAVGSSLKQSRS
Retrocopy TKEYSFLRTSVPRGPKVGSLGLLAHSKEKKNSKSSKIRSLADYRTEDPSDSGGLGSTADAVGSSLKQSRS

Parental  STSVVSEVSPSCETDNRAESASLAGDSVSEADGNESDSSSHSSFSARGACAVLGNVGTPGAAYVVDGQEI
          STSVVSEVSPSCETDNRAESASLAGDSVSEADGNESDSSSHSSFSARGACAVLGNVGTPGAAYVVDGQEI
Retrocopy STSVVSEVSPSCETDNRAESASLAGDSVSEADGNESDSSSHSSFSARGACAVLGNVGTPGAAYVVDGQEI

Parental  SAEALGQFPSIKDVLQAAAAQHQDQNQEANGEVQSRRDSICSSVSMESSFAEPQEELLQILKDKRRLEGQ
          SAEALGQFPSIKDVLQAAAAQHQDQNQEANGEVQSRRDSICSSVSMESSFAEPQEELLQILKDKRRLEGQ
Retrocopy SAEALGQFPSIKDVLQAAAAQHQDQNQEANGEVQSRRDSICSSVSMESSFAEPQEELLQILKDKRRLEGQ

Parental  VEALSLEASQALQEKAELQAQLAALSTRLQAQVEHSHSSQQKQDSLSSEVDTLKQSCWDLERAMTDLQNM
          VEALSLEASQALQEKAELQAQLAALSTRLQAQVEHSHSSQQKQDSLSSEVDTLKQSCWDLERAMTDLQNM
Retrocopy VEALSLEASQALQEKAELQAQLAALSTRLQAQVEHSHSSQQKQDSLSSEVDTLKQSCWDLERAMTDLQNM

Parental  LEAKNASLASSNNDLQVAEEQYQRLMAKVEAMQRNILSKDNTVHDLRQQMTALQSQLQQVQLERTTLTSK
          LEAKNASLASSNNDLQVAEEQYQRLMAKVEAMQRNILSKDNTVHDLRQQMTALQSQLQQVQLERTTLTSK
Retrocopy LEAKNASLASSNNDLQVAEEQYQRLMAKVEAMQRNILSKDNTVHDLRQQMTALQSQLQQVQLERTTLTSK

Parental  LQASQAEITSLQQARQWYQQQLALAQEARVRLQGEMAHIQVGQMTQAGLLEHLKLENVSLSHQLTETQHR
          LQASQAEITSLQQARQWYQQQLALAQEARVRLQGEMAHIQVGQMTQAGLLEHLKLENVSLSHQLTETQHR
Retrocopy LQASQAEITSLQQARQWYQQQLALAQEARVRLQGEMAHIQVGQMTQAGLLEHLKLENVSLSHQLTETQHR

Parental  SIKEKERIAVQLQSIEADMLDQEAAFVQIREAKTMVEEDLQRKLEEFEGEREQLQKVADAAASLEQQLEQ
          SIKEKERIAVQLQSIEADMLDQEAAFVQIREAKTMVEEDLQRKLEEFEGEREQLQKVADAAASLEQQLEQ
Retrocopy SIKEKERIAVQLQSIEADMLDQEAAFVQIREAKTMVEEDLQRKLEEFEGEREQLQKVADAAASLEQQLEQ

Parental  VKLTLFQRDQQLAALQQEHLDVIKQLTSTQEALQAKGQSLDDLQTRYDELQARLEELQREADSREDAIHF
          VKLTLFQRDQQLAALQQEHLDVIKQLTSTQEALQAKGQSLDDLQTRYDELQARLEELQREADSREDAIHF
Retrocopy VKLTLFQRDQQLAALQQEHLDVIKQLTSTQEALQAKGQSLDDLQTRYDELQARLEELQREADSREDAIHF

Parental  LQNEKIVLEVALHSARSDKEELDRGARRLEEDTEETSGLLEQLRQDVAVKSNQVEHLQQETATLRKQMQK
          LQNEKIVLEVALHSARSDKEELDRGAR.LEEDTEETSGLLEQLRQDVAVKSNQVEHLQQETATLRKQMQK
Retrocopy LQNEKIVLEVALHSARSDKEELDRGARCLEEDTEETSGLLEQLRQDVAVKSNQVEHLQQETATLRKQMQK

Parental  VKEQFLQQKVMVEAYRRDAASKDQLINELKATKKRLDSEMKELRQELIKLHGEKKTVEVEHSRLQKDMSL
          VKEQFLQQKVMVEAYRRDAASKDQLINELKATKKRLDSEMKELRQELIKLHGEKKTVEVEHSRLQKDMSL
Retrocopy VKEQFLQQKVMVEAYRRDAASKDQLINELKATKKRLDSEMKELRQELIKLHGEKKTVEVEHSRLQKDMSL

Parental  VHQQMAELEGHLQSVQKERDEMEIHLQSLKFDKEQMIALTEANETLKKQIEELQQEAKKAITEQKQKMKR
          VHQQMAELEGHLQSVQKERDEMEIHLQSLKFDKEQMIALTEANETLKKQIEELQQEAKKAITEQKQKMKR
Retrocopy VHQQMAELEGHLQSVQKERDEMEIHLQSLKFDKEQMIALTEANETLKKQIEELQQEAKKAITEQKQKMKR

Parental  LGSDLTSAQKEMKTKHKAYENAVSILSRRLQEALANKEATDAELNQLRAQSTGGSSDPALHEKIHALEVE
          LGSDLTSAQKEMKTKHKAYENAVSILSRRLQEALANKEATDAELNQLRAQSTGGSSDPALHEKIHALEVE
Retrocopy LGSDLTSAQKEMKTKHKAYENAVSILSRRLQEALANKEATDAELNQLRAQSTGGSSDPALHEKIHALEVE

Parental  LQNVGQSKILLEKELQEVITMTSQELEESREKVLELEDELQESRGFRRKIKRLEESNKKLALELEHERGK
          LQNVGQSKILLEKELQEVITMTSQELEESREKVLELEDELQESRGFR.KIKRLEESNKKLALELEHERGK
Retrocopy LQNVGQSKILLEKELQEVITMTSQELEESREKVLELEDELQESRGFRWKIKRLEESNKKLALELEHERGK

Parental  LTGLGQSNAALREHNSILETALAKREADLVQLNLQVQAVLQRKEEEDRQMKQLVQALQISLEKEKTEVSS
          LTGLGQSNAALREHNSILETALAKREADLVQLNLQVQAVLQRKEEEDRQMKQLVQALQISLEKEKTEVSS
Retrocopy LTGLGQSNAALREHNSILETALAKREADLVQLNLQVQAVLQRKEEEDRQMKQLVQALQISLEKEKTEVSS

Parental  LKEQMAAARVEAGHNRRHFKAATLELSEVKKELQAKEHLVQTLQAEVDELQIQEGKHSQEIAQFQTELAE
          LKEQMAAARVEAGHNRRHFKAATLELSEVKKELQAKEHLVQTLQAEVDELQIQEGKHSQEIAQFQTELAE
Retrocopy LKEQMAAARVEAGHNRRHFKAATLELSEVKKELQAKEHLVQTLQAEVDELQIQEGKHSQEIAQFQTELAE

Parental  ARTQLQLLQKKLEEQRSQQPTGSQEMEDLKWELDQKEREIQSLKQQLDLTEHQGKKELEGTQQTLQTIKS
          ARTQLQLLQKKLEEQRSQQPTGSQEMEDLKWELDQKE.EIQSLKQQLDLTEHQGKKELEGTQQTLQTIKS
Retrocopy ARTQLQLLQKKLEEQRSQQPTGSQEMEDLKWELDQKE*EIQSLKQQLDLTEHQGKKELEGTQQTLQTIKS

Parental  ELETVQEDLSETQKDKFMLQAKVSELKNNMKTLLQQNQQLKLDLRRGAAKKKEPKGESSSSSPATPIKIP
          ELETVQEDLSETQKDKFMLQAKVSELKNNMKTLLQQNQQLKLDLRRGAAKKKEPKGESSSSSPATPIKIP
Retrocopy ELETVQEDLSETQKDKFMLQAKVSELKNNMKTLLQQNQQLKLDLRRGAAKKKEPKGESSSSSPATPIKIP

Parental  DCPVPASLLEELLRPPPAVSKEPLKNLNSCLQQLKQEMDSLQRQMEEHTITVHESLSSWAQVEAAPAEHA
          DCPVPASLLEELLRPPPAVSKEPLKNLNSCLQQLKQEMDSLQRQMEEHTITVHESLSSWAQVEAAPAEHA
Retrocopy DCPVPASLLEELLRPPPAVSKEPLKNLNSCLQQLKQEMDSLQRQMEEHTITVHESLSSWAQVEAAPAEHA

Parental  HARGDTKVHNQNSVPGEGLGQ
          HARGDTKVHNQNSVPGEGLGQ
Retrocopy HARGDTKVHNQNSVPGEGLGQ

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	0.36 RPM	14.16 RPM
SRP017611_kidney	0.07 RPM	13.54 RPM
SRP017611_liver	0.00 RPM	9.61 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2044 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2044 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2044 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000037437	1 retrocopy	retro_rnor_2044 ,