RetrogeneDB ID: retro_rnor_1387

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:25079347..25080223(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000046506
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Creb1
• Ensembl ID: ENSRNOG00000013412
• Aliases: Creb1, Creb
• Description: Cyclic AMP-responsive element-binding protein 1 [Source:UniProtKB/Swiss-Prot;Acc:P15337]

Sequence

>retro_rnor_1387
ATGACCATGGACTCTGGAGCAGACAACCAGCAGAGTGGAGATGCTGCTGTAACAGAAGCTGAAAGTCAACAAATGACAGT
TCAAGCCCAGCCACAGATTGCCACATTAGCCCAGGTATCCATGCCAGCAGCTCATGCGACGTCATCTGCTCCCACTGTAA
CCTTAGTGCAGCTGCCCAATGGGCAGACAGTCCAGGTCCATGGGGTCATCCAGGCGGCCCAGCCATCAGTTATTCAGTCT
CCACAAGTCCAAACAGTTCAGATTTCAACTATTGCAGAAAGTGAAGATTCACAGGAGTCTGTGGATAGTGTAACTGATTC
CCAAAAATGAAGGGAAATCCTTTCAAGGAGGCCTTCCTACAGGAAAATTTTGAATGACTTATCTTCTGATGCACCAGGGG
TGCCAAGGATTGAAGAAGAAAAATCAGAAGAAGAGACTTCAGCCCCTGCCATCACCACTGTAACAGTGCCAACCCCGATT
TACCAAACTAGCAGTGGGCAGTATATTGCCATTACCCAGGGAGGAGCAATACAGCTGGCTAACAATGGTACCGATGGGGT
ACAGGGCCTGCAGACACTAACCATGACCAATGCAGCTGCCACTCAGCCGGGTACTACCATTCTACAATATGCACAGACCA
CTGATGGACAGCAGATTCTAGTGCCCAGCAACCAAGTTGTTGTTCAAGCTGCCTCTGGTGATGTACAAACATACCAGATT
CGCACAGCACCCACTAGCACCATTGCCCCTGGAGTTGTTATGGTGTCCTCCCCAGCACTTCCTACACAGCCTGCTGAAGA
AGCAGCACGAAAGAGAGAGGTTCGTCTAATGAAGAACAGGGAAGCAGCAAGAGAATGTCGTAGAAAGAAGAAAGAA

Alignment

ORF - retro_rnor_1387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.32 %
• Parental protein coverage: 89.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTMDSGADNQQSGDAAVTEAESQQMTVQAQPQIATLAQVSMPAAHATSSAPTVTLVQLPNGQTVQVHGVI
          MTMDSGADNQQSGDAAVTEAESQQMTVQAQPQIATLAQVSMPAAHATSSAPTVTLVQLPNGQTVQVHGVI
Retrocopy MTMDSGADNQQSGDAAVTEAESQQMTVQAQPQIATLAQVSMPAAHATSSAPTVTLVQLPNGQTVQVHGVI

Parental  QAAQPSVIQSPQVQTVQISTIAESEDSQESVDSVTDSQKRREILSRRPSYRKILNDLSSDAPGVPRIEEE
          QAAQPSVIQSPQVQTVQISTIAESEDSQESVDSVTDSQK.REILSRRPSYRKILNDLSSDAPGVPRIEEE
Retrocopy QAAQPSVIQSPQVQTVQISTIAESEDSQESVDSVTDSQK*REILSRRPSYRKILNDLSSDAPGVPRIEEE

Parental  KSEEETSAPAITTVTVPTPIYQTSSGQYIAITQGGAIQLANNGTDGVQGLQTLTMTNAAATQPGTTILQY
          KSEEETSAPAITTVTVPTPIYQTSSGQYIAITQGGAIQLANNGTDGVQGLQTLTMTNAAATQPGTTILQY
Retrocopy KSEEETSAPAITTVTVPTPIYQTSSGQYIAITQGGAIQLANNGTDGVQGLQTLTMTNAAATQPGTTILQY

Parental  AQTTDGQQILVPSNQVVVQAASGDVQTYQIRTAPTSTIAPGVVMASSPALPTQPAEEAARKREVRLMKNR
          AQTTDGQQILVPSNQVVVQAASGDVQTYQIRTAPTSTIAPGVVM.SSPALPTQPAEEAARKREVRLMKNR
Retrocopy AQTTDGQQILVPSNQVVVQAASGDVQTYQIRTAPTSTIAPGVVMVSSPALPTQPAEEAARKREVRLMKNR

Parental  EAARECRRKKKE
          EAARECRRKKKE
Retrocopy EAARECRRKKKE

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	0.00 RPM	15.46 RPM
SRP017611_kidney	0.00 RPM	16.26 RPM
SRP017611_liver	0.13 RPM	9.41 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1387 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1387 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1387 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000007374	3 retrocopies	retro_meug_1195, retro_meug_2029, retro_meug_596,
Rattus norvegicus	ENSRNOG00000013412	1 retrocopy	retro_rnor_1387 ,