RetrogeneDB ID: retro_rnor_2396

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:119513979..119515107(-)
• Located in intron of: ENSRNOG00000010227

Retrocopy information

• Ensembl ID: ENSRNOG00000050817
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ddx41
• Ensembl ID: ENSRNOG00000012771
• Aliases: None
• Description: probable ATP-dependent RNA helicase DDX41 [Source:RefSeq peptide;Acc:NP_001101516]

Sequence

>retro_rnor_2396
ATTCTGTCTGGTCGGGACATGATTGGCATCGCCTTCACGGGGTCAGGCAAGACACTGGTATTCACACTGCCCGTCATCAT
GTTCTGCCTGGAACAAGAGAAGCGGCTGCCTTTCTCCAAGCGGGAAGGACCTTATGGACTCATCATCTGCCCCTCGCGAG
AGCTGGCTCGGCAGACCCATGGCATCCTGGAGTATTACTGCCGTCTGCTGCAGGAAGACAGCTCCCCTCTCCTGCACTGC
GCGCTCTGCATCGGGGGCGTGTCGGTGAAGGAGCAGATGGAGACCATGCGACATGGTGTCCACATCATGGTAGCCACAAC
GGGCCGCCTCATGGATTTGCTGCAGAAGAAAATGGTCAGCCTAGACATCTGCCGCTACCTGGCCCTGGATGAGGCTGACC
GCATGATCGACATGGGCTTTGAGGGTGACATCCGTACCATCTTCTCCTACTTCAAGGGCCAGCGGCAGACTCTGCTCTTC
AGTGCCACCATGCCGAAGAAGATTCAGAACTTCGCCAAAAGTGCTCTGGTCAAGCCCGTCACCATCAATGTTGGTCGTGC
TGGAGCAGCCAGCCTTGACGTCATCCAGGAGGTGGAATATGTGAAGGAGGAAGCCAAGATGGTGTACCTGCTTGAGTGCT
TGCAGAAGACGCCCCCACCTGTACTCATCTTTGCAAAGAAGAAAGCAGATGTGGATGCCATTCACGAATACCTCCTGCTC
AAAGGAGTTGAGGCTGTGGCCATTCATGGGGGCAAAGACCAGGAAGAGCGGACCAAGGCCATTGAGGCATTCCGGGAAGG
CAAGAAGGACGTCTTAGTGGCCACGGACGTGGCCTCTAAAGGCCTAGACTTTCCTGCCATCCAGCACGTCATCAACTATG
ACATGCCTGAAGAAATCGAGAACTATGTGCACCGAATTGGCCGCACTGGGCGCTCGGGAAACACAGGCATCGCCACCACC
TTTATCAACAAGGCCTGCGATGAGTCAGTGCTCATGGACCTCAAAGCCTTGTTGCTGGAGGCCAAGCAGAAGGTACCACC
TGTTCTGCAAGTGCTGCACTGTGGGGATGAGTCCATGCTGGACGTCGGAGGAGAACGGGGCTGCACCTTCTGTGGAGGCC
TTGGTCAT

Alignment

ORF - retro_rnor_2396 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.62 %
• Parental protein coverage: 60.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL
          ILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL
Retrocopy ILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLL

Parental  QEDSSPLLRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMIDMGF
          QEDSSPLL.CALCIGG.SVKEQMET.RHGVH.MVAT.GRLMDLLQKKMVSLDICRYLALDEADRMIDMGF
Retrocopy QEDSSPLLHCALCIGGVSVKEQMETMRHGVHIMVATTGRLMDLLQKKMVSLDICRYLALDEADRMIDMGF

Parental  EGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLDVIQEVEYVKEEAKMVYL
          EGDIRTIFSYFKGQRQTLLFSATMPKKIQ................RAGAASLDVIQEVEYVKEEAKMVYL
Retrocopy EGDIRTIFSYFKGQRQTLLFSATMPKKIQXXXXXXXXXXXXXXXXRAGAASLDVIQEVEYVKEEAKMVYL

Parental  LECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK
          LECLQKTPPPVLIFA.KKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK
Retrocopy LECLQKTPPPVLIFAKKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASK

Parental  GLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQ
          GLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQ
Retrocopy GLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQ

Parental  VLHCGDESMLDIGGERGCAFCGGLGH
          VLHCGDESMLD.GGERGC.FCGGLGH
Retrocopy VLHCGDESMLDVGGERGCTFCGGLGH

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	0.14 RPM	27.03 RPM
SRP017611_kidney	0.07 RPM	44.17 RPM
SRP017611_liver	0.00 RPM	17.01 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2396 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2396 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008770	1 retrocopy	retro_cpor_1521,
Loxodonta africana	ENSLAFG00000026418	1 retrocopy	retro_lafr_689,
Macropus eugenii	ENSMEUG00000014375	1 retrocopy	retro_meug_2040,
Otolemur garnettii	ENSOGAG00000011123	1 retrocopy	retro_ogar_1801,
Rattus norvegicus	ENSRNOG00000012771	1 retrocopy	retro_rnor_2396 ,
Sarcophilus harrisii	ENSSHAG00000014005	1 retrocopy	retro_shar_53,