RetrogeneDB ID: retro_rnor_587

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:77940757..77942746(-)
• Located in intron of: ENSRNOG00000046091

Retrocopy information

• Ensembl ID: ENSRNOG00000048028
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Srp72
• Ensembl ID: ENSRNOG00000002100
• Aliases: None
• Description: signal recognition particle 72 kDa protein [Source:RefSeq peptide;Acc:NP_001164072]

Sequence

>retro_rnor_587
GGTGTCAGTCCCTGCGCGCTGTGGAGTGAGGTGAACGGTTATGGGCAGAACAGCGACTTCTCGCGTGCCCTCAAGACCGT
CAACAAAATATTGCAGATCAACAAGGATGATGTCACGGCCTTGCACTGTAAAGTTGTTTGCCTTATCCAGAATGGAAGTT
TCAAAGAAGCCTTGAATGTCATCAATACTCACACCAAAGTGTTAGCCAATAACTCTCTGTCCTTTGAGAAGGCATATTGC
GAGTACAGGTTGAACAGAATCGAGAATGCCTTGAAGACAATAGAAAGTGCCAACCAGCAGACAGACAAACTGAAGGAGCT
TTATGGACAAGTTGTGTACCGCCTGGAACGCTACGATGAGTGCCTGGCAGTGTACCGAGATCTTGTCCGCAACTCCCAGT
ATGACTACGATGAGGAGAGGAAGACAAACCTGTCAGCGGTCGTTGCCGCTCAAAGCAACTGGGAAAAAGTGGTTCCCGAG
AACTTAGGTCTCCAAGAAGGCACACACGAACTCTGTTACAACGCTGCGTGTGCACTGATAAGGCAAGGCCAGCTGACCCA
GGCAATGAAAATCCTACAAAAGGCTGAAGATCTTTGTTGCCGTTCATTTTCAGAAGATTCAGATGGGACTGAGGAAGACC
CTCAGACCGAGCTGGCCATCATTCACGATCAAATGGCTTACATCATGCAGCTTCAGGGGCGCATCGAGGAGGCTCTGCAG
CTTTACAATCAGATAATAAAACTGAAGCCAACAGATGTGGCACTTCTTGCTGTAATTGCATATAATATCATTACCATTAA
TAAGGACCAAAATGTCTTTGACTCCAAGAAGAAAGTGAAATTAACCAATGCAGAAGGAGTGGAGTTTAAGCTCTCCAAGA
GACAGCTTCAAGCCATAGAGTTCAACAAGGCTTTGCTTGCCATGTATACAAACCAGGCAGAACGATGCCGAAAAATAGCT
TCTAGCTTGCAGTCCCAGAGTCCTGAGCATCTCCTGCCTGTGCTGATCCAAGCTGCCCAGCTCTGTCGTGAAAAGCAGCA
TACAAAGGCAATAGAGCTGCTTCAGGAATTTTCTGATCAACATCCAGAAAATGCAGCTGAAATCAAGCTTACCATGGCTC
AATTGAAAATTTCCCAAGGTAATATTTCCAAAGCGTGCCTAATACTGAGAAGCATAGAGGAATTAAAGCATAAGTCAGGC
ATGGTATCCGCGTTGGTGACCATGTACAGCCACGAGGAAGACTTTGAGAGTGCCATTGAAGTCTTCACACAGGCTATCCA
GTGGTATCAAAGCCATCAGTCCAAGTCCCCTGCTCATTTGTCCTTGATAAGAGAGGCTGCAAAGTTCAAGCTCAAATATG
AACGGAAGAAGGAGGCAGTTAGTGACCTAGAGCAGCTGTGGAAACAAAATTCAAAAGATATTCACACGCTAGCCCAGCTT
ATCTCTGCTTACTCGCTTGTGGATCCAGAGAAAGCAAAGGCTCTTAGTAAACACCTGCCCTCATCGGATAGTATGTCTCT
AAAGGTAGATGTTGAGGCTCTTGAGAATTCTCCTGGTGCTACATACATTCGGAAGAAGGGTGGAAAAGTTACTGGAGATA
ATCAACCAAAGGAACAAGGACAGGGAGATTTGACAAAGAAGAAGAAAAAGAAAGGAAAACTGCCTAAGAATTATGACCCA
AAAGTTACCCCAGATCCAGAAAGACGGCTACCAATGCGAGAGTGCTCTTACTACCGAGGAAGAAAGAAGGGCAAAAAGAA
GGACCAGATCGGAAAAGGAACACAGGGAGCGATCGCAGGAGCCTCCTCTGAGTTGGACGCCAGTAAAACTGTGAGCAGCC
CACCCACCTCCCCAAGACCCGGCAGTGCGGCAACGATGGCCTCCTCTACAAGTAACATTGTACCCCCAAGACACCAGAAA
CCCGCAGGGGCCCCAGCAACGAAAATGAAGCAGCAACAGAAGAAGAAGAAAGGAGGGAAAAGTGGTTGG

Alignment

ORF - retro_rnor_587 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.19 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVSVPALWSEVNRYGQNSDFTRALKTVNKILQINKDDVTALHCKVVCLIQNGSFKEALNVINTHTKVLAN
          GVS..ALWSEVN.YGQNSDF.RALKTVNKILQINKDDVTALHCKVVCLIQNGSFKEALNVINTHTKVLAN
Retrocopy GVSPCALWSEVNGYGQNSDFSRALKTVNKILQINKDDVTALHCKVVCLIQNGSFKEALNVINTHTKVLAN

Parental  NSLSFEKAYCEYRLNRIENALKTIESANQQTDKLKELYGQVLYRLERYDECLAVYRDLVRNSQDDYDEER
          NSLSFEKAYCEYRLNRIENALKTIESANQQTDKLKELYGQV.YRLERYDECLAVYRDLVRNSQ.DYDEER
Retrocopy NSLSFEKAYCEYRLNRIENALKTIESANQQTDKLKELYGQVVYRLERYDECLAVYRDLVRNSQYDYDEER

Parental  KTNLSAVVAAQSNWEKVVPENLGLQEGTHELCYNAACALIGQGQLTQAMKILQKAEDLCRRSFSEDSDGT
          KTNLSAVVAAQSNWEKVVPENLGLQEGTHELCYNAACALI.QGQLTQAMKILQKAEDLC.RSFSEDSDGT
Retrocopy KTNLSAVVAAQSNWEKVVPENLGLQEGTHELCYNAACALIRQGQLTQAMKILQKAEDLCCRSFSEDSDGT

Parental  EEDPQAELAIIHGQMAYIMQLQGRIEEALQLYNQIIKLKPTDVALLAVIANNIITINKDQNVFDSKKKVK
          EEDPQ.ELAIIH.QMAYIMQLQGRIEEALQLYNQIIKLKPTDVALLAVIA.NIITINKDQNVFDSKKKVK
Retrocopy EEDPQTELAIIHDQMAYIMQLQGRIEEALQLYNQIIKLKPTDVALLAVIAYNIITINKDQNVFDSKKKVK

Parental  LTNAEGVEFKLSKRQLQAIEFNKALLAMYTNQAERCRKIASSLQSQSPEHLLPVLIQAAQLCREKQHTKA
          LTNAEGVEFKLSKRQLQAIEFNKALLAMYTNQAERCRKIASSLQSQSPEHLLPVLIQAAQLCREKQHTKA
Retrocopy LTNAEGVEFKLSKRQLQAIEFNKALLAMYTNQAERCRKIASSLQSQSPEHLLPVLIQAAQLCREKQHTKA

Parental  IELLQEFSDQHPENAAEIKLTMAQLKISQGNISKACLILRSIEELKHKSGMVSALVTMYSHEEDFESAIE
          IELLQEFSDQHPENAAEIKLTMAQLKISQGNISKACLILRSIEELKHKSGMVSALVTMYSHEEDFESAIE
Retrocopy IELLQEFSDQHPENAAEIKLTMAQLKISQGNISKACLILRSIEELKHKSGMVSALVTMYSHEEDFESAIE

Parental  VFTQAIQWYQSHQSKSPAHLSLIREAAKFKLKYERKKEAVSDLEQLWKQNSKDIHTLAQLISAYSLVDPE
          VFTQAIQWYQSHQSKSPAHLSLIREAAKFKLKYERKKEAVSDLEQLWKQNSKDIHTLAQLISAYSLVDPE
Retrocopy VFTQAIQWYQSHQSKSPAHLSLIREAAKFKLKYERKKEAVSDLEQLWKQNSKDIHTLAQLISAYSLVDPE

Parental  KAKALSKHLPSSDSMSLKVDVEALENSPGATYIRKKGGKVTGDNQPKEQGQGDLTKKKKKKGKLPKNYDP
          KAKALSKHLPSSDSMSLKVDVEALENSPGATYIRKKGGKVTGDNQPKEQGQGDLTKKKKKKGKLPKNYDP
Retrocopy KAKALSKHLPSSDSMSLKVDVEALENSPGATYIRKKGGKVTGDNQPKEQGQGDLTKKKKKKGKLPKNYDP

Parental  KVTPDPERRLPMRECSYYRGRKKGKKKDQIGKGTQGAIAGASSELDASKTVSSPPTSPRPGSAATMASST
          KVTPDPERRLPMRECSYYRGRKKGKKKDQIGKGTQGAIAGASSELDASKTVSSPPTSPRPGSAATMASST
Retrocopy KVTPDPERRLPMRECSYYRGRKKGKKKDQIGKGTQGAIAGASSELDASKTVSSPPTSPRPGSAATMASST

Parental  SNIVPPRHQKPAGAPATKKKQQQKKKKGGKSGW
          SNIVPPRHQKPAGAPATK.KQQQKKKKGGKSGW
Retrocopy SNIVPPRHQKPAGAPATKMKQQQKKKKGGKSGW

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	33.72 RPM
SRP017611_kidney	0.14 RPM	31.05 RPM
SRP017611_liver	0.07 RPM	30.79 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_587 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_587 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_587 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017998	1 retrocopy	retro_cjac_2538,
Homo sapiens	ENSG00000174780	2 retrocopies	retro_hsap_1939, retro_hsap_3685,
Nomascus leucogenys	ENSNLEG00000008806	1 retrocopy	retro_nleu_2909,
Oryctolagus cuniculus	ENSOCUG00000012226	1 retrocopy	retro_ocun_989,
Rattus norvegicus	ENSRNOG00000002100	1 retrocopy	retro_rnor_587 ,