RetrogeneDB ID: retro_rnor_1663

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:185687430..185688541(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000028120
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Psat1
• Ensembl ID: ENSRNOG00000013971
• Aliases: Psat1, Psa1
• Description: phosphoserine aminotransferase [Source:RefSeq peptide;Acc:NP_942033]

Sequence

>retro_rnor_1663
ATGGAAGCCACCAAGCAAGTGATTAACTTTGGGCCCGGGCCTGCCAAGTTACGATACTCGGTTTTGTTAGAGATACAGAA
GCTGCTACTAGACTACAAAGGCCTTGGCATCAACGTGCTTGAAATGAGTCACAGGTCATCAGATTTCGCCAAGATTATTA
GCAACACAGAGAATCTTGTGAGGGAATTGCTAGCTGTTCCCAACAACTACAAGGTGATCTTTGTACAAGGAGGTGGGACT
GGCCAGTTCAGTGCCGTCCCTTTAAATCTTACTGGCCTGAAAGCTGGAAGGTGTGCCCACTATGTGGTGACCGGAGCTTG
GTCAGCTAAGGCTGCGGAAGAAGCCAAGAAGTTTGGGACTGTGAACATTGTTCATCCTAAACTTGGAAATTACACAAAAA
TTCCAGACCCAAGCACCTGGAACCTCAACCCAGACACCTCCTATGTGTACCTCTGTGCAAACGAGACTGTGCATGGCGTG
GAGTTTGACTTCATACCTGACATCAAGGGAGCAGTGCTGGTCTGTGACATGTCTTCAAACTTCTTATCCAGGCCAGTGGA
CGTTTCCAAGTTTGGTGTGATTTTCGCTGGTGCTCAGAAGAATGTTGGCTCTGCTGGGGTGACGGTGGTAATTGTCTGTG
ATGACCTGCTGGGGTTCGCCCTCAGAGAGTGCCCATCAGTCCTTGACTACAAAGTGCAGGCTGGGAACAACTCTTGTTAT
AACACACCTCCATGCTTCAGCATCTACGTCATGGGCATGGTCCTGGAATGGATCGAGAACAATGGTGGGGCCGCAGCCAT
GGAGAAGCTCAGCTCCGTCAAATCCCAAATGATTTATGAGATTATTGATAATTCTCAAGGATTTTATGTTGTGTCCGGTG
GAGCGCCAGAATAGAAGCAGGATGAACATTCCGTTTCGCATTGGCAAAGGCAAAGGGAATGAAGCTCTGGAGAAGCGGTT
TCTTGATAAGGCCGTAGAACTCAACATGATCTCCTTGAAGCGGCACAGGTCGGTGGGAGGCATCCGAGCCTCTCTGTATA
ATGCTGTCACCACCGAAGATGTTGAGAAGTTGGCTGCCTTCATGAAGAACTTTTTGGAGATGCATCAGCTG

Alignment

ORF - retro_rnor_1663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEATKQVVNFGPGPAKLPYSVLLEIQKQLLDYKGLGISVLEMSHRSPDFAKIISNTENLVRELLAVPNNY
          MEATKQV.NFGPGPAKL.YSVLLEIQK.LLDYKGLGI.VLEMSHRS.DFAKIISNTENLVRELLAVPNNY
Retrocopy MEATKQVINFGPGPAKLRYSVLLEIQKLLLDYKGLGINVLEMSHRSSDFAKIISNTENLVRELLAVPNNY

Parental  KVIFVQGGGTGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTVNIVHPKLGSYTKIPDPSTW
          KVIFVQGGGTGQFSAVPLNL.GLKAGRCA.YVVTGAWSAKAAEEAKKFGTVNIVHPKLG.YTKIPDPSTW
Retrocopy KVIFVQGGGTGQFSAVPLNLTGLKAGRCAHYVVTGAWSAKAAEEAKKFGTVNIVHPKLGNYTKIPDPSTW

Parental  NLNPDASYVYFCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSRPVDVSKFGVIFAGAQKNVGSAGVTVV
          NLNPD.SYVY.CANETVHGVEFDFIPD.KGAVLVCDMSSNFLSRPVDVSKFGVIFAGAQKNVGSAGVTVV
Retrocopy NLNPDTSYVYLCANETVHGVEFDFIPDIKGAVLVCDMSSNFLSRPVDVSKFGVIFAGAQKNVGSAGVTVV

Parental  IVRDDLLGFALRECPSVLDYKVQAGNNSLYNTPPCFSIYVMDMVLEWIKNNGGAAAMEKLSSVKSQMIYE
          IV.DDLLGFALRECPSVLDYKVQAGNNS.YNTPPCFSIYVM.MVLEWI.NNGGAAAMEKLSSVKSQMIYE
Retrocopy IVCDDLLGFALRECPSVLDYKVQAGNNSCYNTPPCFSIYVMGMVLEWIENNGGAAAMEKLSSVKSQMIYE

Parental  IIDNSQGFYV-CPVERQNRSRMNIPFRIGNSKGDEALEKRFLDKAVELNMISLKGHRSVGGIRASLYNAV
          IIDNSQGFYV.CPVERQNRSRMNIPFRIG..KG.EALEKRFLDKAVELNMISLK.HRSVGGIRASLYNAV
Retrocopy IIDNSQGFYV>CPVERQNRSRMNIPFRIGKGKGNEALEKRFLDKAVELNMISLKRHRSVGGIRASLYNAV

Parental  TTEDVEKLAAFLRSFLVVHVL
          TTEDVEKLAAF...FL..H.L
Retrocopy TTEDVEKLAAFMKNFLEMHQL

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	1.08 RPM	71.68 RPM
SRP017611_kidney	1.12 RPM	134.26 RPM
SRP017611_liver	0.00 RPM	3.23 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1663 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1663 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1663 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006898	1 retrocopy	retro_amel_375,
Bos taurus	ENSBTAG00000013960	1 retrocopy	retro_btau_1658,
Canis familiaris	ENSCAFG00000001570	1 retrocopy	retro_cfam_269,
Choloepus hoffmanni	ENSCHOG00000003817	1 retrocopy	retro_chof_2702,
Callithrix jacchus	ENSCJAG00000003319	1 retrocopy	retro_cjac_1203,
Echinops telfairi	ENSETEG00000004158	1 retrocopy	retro_etel_99,
Homo sapiens	ENSG00000135069	3 retrocopies	retro_hsap_2267, retro_hsap_4054, retro_hsap_412,
Gorilla gorilla	ENSGGOG00000015480	1 retrocopy	retro_ggor_407,
Loxodonta africana	ENSLAFG00000017917	2 retrocopies	retro_lafr_1249, retro_lafr_660,
Macaca mulatta	ENSMMUG00000011868	2 retrocopies	retro_mmul_1029, retro_mmul_2341,
Mustela putorius furo	ENSMPUG00000012566	1 retrocopy	retro_mputfur_808,
Nomascus leucogenys	ENSNLEG00000002989	3 retrocopies	retro_nleu_1010, retro_nleu_1288, retro_nleu_2805,
Oryctolagus cuniculus	ENSOCUG00000007765	1 retrocopy	retro_ocun_1092,
Pongo abelii	ENSPPYG00000019313	3 retrocopies	retro_pabe_1950, retro_pabe_308, retro_pabe_3328,
Pan troglodytes	ENSPTRG00000021045	2 retrocopies	retro_ptro_1606, retro_ptro_316,
Rattus norvegicus	ENSRNOG00000013971	1 retrocopy	retro_rnor_1663 ,
Tupaia belangeri	ENSTBEG00000012946	1 retrocopy	retro_tbel_1577,
Tarsius syrichta	ENSTSYG00000000093	2 retrocopies	retro_tsyr_1073, retro_tsyr_1212,