RetrogeneDB ID: retro_ocun_684

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:6090815..6092930(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STT3A
• Ensembl ID: ENSOCUG00000014677
• Aliases: None
• Description: STT3A, subunit of the oligosaccharyltransferase complex (catalytic) [Source:HGNC Symbol;Acc:6172]

Sequence

>retro_ocun_684
ATGACTAAGCTTGGATTTTTGCGGTTGTCCTATGAGAAGCAGGACACACTTCTGAAGCTTCTCATTCTGCCAATGGCTGC
TGTGTTATCTTTCTCCACTCGTCTCTTTGCTGTCCTGAGATTTGAAAGTGTTATCCATGAATTTGATCCGTACTTTAATT
ATCGGACTACCCGGTTCCTGGCCGAGGAGGGGTTTTATAAATTCCATAACTGGTTTGATGACCGGGCCTGGTACCCTTTG
GGACGAATCATAGGAGGAACAATATACCCAGGCTTAATGATTACCTCTGCTGCAATCTACCATGTGCTGCACTTTTTCCA
CATCACCATTGACATTCGGAATGTCTGTGTGTTCCTGGCCCCTCTCTTCTCCTCCTTCACTACCATCGTCACGTACCACC
TTACCAAAGAGCTCAAGGATGCAGGGGCTGGGCTGCTTGCTGCTGCCATGATAGCTGTTGTCCCTGGATATATCTCCTGA
TCTGTGGTTGGCTCCTATGATAATGAAGGGATTGCCATTTTTTGTATGCTGCTTACCTACTACATGTGGATCAAGGCAGT
AAAGACTGGTTCTATCTATTGGGCAGCCAAGTGTGCCCTTGCTTATTTCTATATGGTCTCTTCATGGGGGGGTTATGTGT
TCCTGATCAACTTGATCCCGCTCCACGTCCTGGTGCTGATGCTCACAGGCCGTTTCTCCCATCGAATCTACGTGGCTTAC
TGTACCGTCTACTGCCTGGGTACCATACTTTCCAAGCAGATCTCCTTTGTGGGTTTCCAGCCTGTCCTTTCGTCGGAGCA
CATGGCAGCCTTTGGGGTCTTTGGCCTCTGCCAGATACATGCCTTTGTGGATTACCTGCGCAGCAAGTTGAACCCACAGC
AATTTGAAGTTCTTTTCCGCAGTGTCATCCCCTTGGTGGGCTTTGTCCTTCTCACAATGGGAGCTCTCCTCATGCTGACA
GGAAAAATATCTCCCTGGACGGGCCGTTTCTACTCACTGCTGGATCCTTCTTATGCTAAGAACAACATCCCCATCATTGC
ATCTGTATCTGAGCATCAGCCCACAACCTGGTCCTCCTACTATTTTGACTTGCAGCTCCTCGTCTTCATGTTTCCAGTTG
GCCTCTATTACTGCTTTAGCAACCTGTCTGATGCCCGGATTTTTATCATCATGTATGGTGTGACCAGCATGTACTTTTCA
GCTGTGATGTGCGTCTGATGTTGGTGTTGGCGCCTGTTATGTGCATTCTTTCTGGCATTGGAGTTTCCCAGGTGCTATCC
ACATATATGAAGAATCTGGACATAAGTCGTCCAGACAAGAAGAGCAAGAAGCAACAGGATTCTACATACCCTATTAAGAA
TGAAGTGGCAAGTGGGATGATATTGGTCATGGCCTTCTTTCTCATTACCTACACCTTTCATTCAACCTGGGTGACCAGTG
AGGCCTACTCTTCTCCCTCCATTGTGCTGTCTGCCCGGGGTGGGGATGGCAGTAGGATCATTTTTGATGACTTCCGAGAA
GCGTATTATTGGCTTCGTCACAATACTCCAGAGGATGCAAAAGTCATGTCATGGTGGGATTACGGCTACCAGATTACAGC
TATGGCAAATCGGACAATTTTAGTGGACAACAACACATGGAATAATACCCATATTTCTCGAGTAGGGCAGGCAATGGCAT
CCACAGAAGAAAAAGCCTATGAAATCATGAGGGAGCTTGATGTCAGCTATGTGTTGGTCATTTTTGGAGGCCTCACTGGG
TATTCCTCTGATGATATCAACAAATTTCTTTGGATGGTTCGGATTGGAGGCAGCACAGACACAGGCAAACATATCAAGGA
GAATGACTATTATACTCCAACTGGGGAATTCCGTGTGGGACCGTGAGGGTTCTCCAGTGCTGCTCAACTGTCTCATGTAC
AAGATGTGTTACTACCGCTTTGGACAGGTCTACACAGAAGCTAAGCGTCCACCAGGCTTTGACCGTGTCCGAAATGCTGA
GATTGGGAATAAAGACTTTGAGCTTGATGTGCTGGAGGAGGCATATACCACAGAACACTGGCTGGTCAGGATATACAAGG
TAAAGGACCTGGATAATCGAGGCTTGTCAAGGACA

Alignment

ORF - retro_ocun_684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTKLGFLRLSYEKQDTLLKLLILSMAAVLSFSTRLFAVLRFESVIHEFDPYFNYRTTRFLAEEGFYKFHN
          MTKLGFLRLSYEKQDTLLKLLIL.MAAVLSFSTRLFAVLRFESVIHEFDPYFNYRTTRFLAEEGFYKFHN
Retrocopy MTKLGFLRLSYEKQDTLLKLLILPMAAVLSFSTRLFAVLRFESVIHEFDPYFNYRTTRFLAEEGFYKFHN

Parental  WFDDRAWYPLGRIIGGTIYPGLMITSAAIYHVLHFFHITIDIRNVCVFLAPLFSSFTTIVTYHLTKELKD
          WFDDRAWYPLGRIIGGTIYPGLMITSAAIYHVLHFFHITIDIRNVCVFLAPLFSSFTTIVTYHLTKELKD
Retrocopy WFDDRAWYPLGRIIGGTIYPGLMITSAAIYHVLHFFHITIDIRNVCVFLAPLFSSFTTIVTYHLTKELKD

Parental  AGAGLLAAAMIAVVPGYISRSVAGSYDNEGIAIFCMLLTYYMWIKAVKTGSIYWAAKCALAYFYMVSSWG
          AGAGLLAAAMIAVVPGYIS.SV.GSYDNEGIAIFCMLLTYYMWIKAVKTGSIYWAAKCALAYFYMVSSWG
Retrocopy AGAGLLAAAMIAVVPGYIS*SVVGSYDNEGIAIFCMLLTYYMWIKAVKTGSIYWAAKCALAYFYMVSSWG

Parental  GYVFLINLIPLHVLVLMLTGRFSHRIYVAYCTVYCLGTILSMQISFVGFQPVLSSEHMAAFGVFGLCQIH
          GYVFLINLIPLHVLVLMLTGRFSHRIYVAYCTVYCLGTILS.QISFVGFQPVLSSEHMAAFGVFGLCQIH
Retrocopy GYVFLINLIPLHVLVLMLTGRFSHRIYVAYCTVYCLGTILSKQISFVGFQPVLSSEHMAAFGVFGLCQIH

Parental  AFVDYLRSKLNPQQFEVLFRSVISLVGFVLLTVGALLMLTGKISPWTGRFYSLLDPSYAKNNIPIIASVS
          AFVDYLRSKLNPQQFEVLFRSVI.LVGFVLLT.GALLMLTGKISPWTGRFYSLLDPSYAKNNIPIIASVS
Retrocopy AFVDYLRSKLNPQQFEVLFRSVIPLVGFVLLTMGALLMLTGKISPWTGRFYSLLDPSYAKNNIPIIASVS

Parental  EHQPTTWSSYYFDLQLLVFMFPVGLYYCFSNLSDARIFIIMYGVTSMYFSAVM-VRLMLVLAPVMCILSG
          EHQPTTWSSYYFDLQLLVFMFPVGLYYCFSNLSDARIFIIMYGVTSMYFSAVM.VRLMLVLAPVMCILSG
Retrocopy EHQPTTWSSYYFDLQLLVFMFPVGLYYCFSNLSDARIFIIMYGVTSMYFSAVM<VRLMLVLAPVMCILSG

Parental  IGVSQVLSTYMKNLDISRPDKKSKKQQDSTYPIKNEVASGMILVMAFFLITYTFHSTWVTSEAYSSPSIV
          IGVSQVLSTYMKNLDISRPDKKSKKQQDSTYPIKNEVASGMILVMAFFLITYTFHSTWVTSEAYSSPSIV
Retrocopy IGVSQVLSTYMKNLDISRPDKKSKKQQDSTYPIKNEVASGMILVMAFFLITYTFHSTWVTSEAYSSPSIV

Parental  LSARGGDGSRIIFDDFREAYYWLRHNTPEDAKVMSWWDYGYQITAMANRTILVDNNTWNNTHISRVGQAM
          LSARGGDGSRIIFDDFREAYYWLRHNTPEDAKVMSWWDYGYQITAMANRTILVDNNTWNNTHISRVGQAM
Retrocopy LSARGGDGSRIIFDDFREAYYWLRHNTPEDAKVMSWWDYGYQITAMANRTILVDNNTWNNTHISRVGQAM

Parental  ASTEEKAYEIMRELDVSYVLVIFGGLTGYSSDDINKFLWMVRIGGSTDTGKHIKENDYYTPTGEFRV-DR
          ASTEEKAYEIMRELDVSYVLVIFGGLTGYSSDDINKFLWMVRIGGSTDTGKHIKENDYYTPTGEFRV.DR
Retrocopy ASTEEKAYEIMRELDVSYVLVIFGGLTGYSSDDINKFLWMVRIGGSTDTGKHIKENDYYTPTGEFRV>DR

Parental  EGSPVLLNCLMYKMCYYRFGQVYTEAKRPPGFDRVRNAEIGNKDFELDVLEEAYTTEHWLVRIYKVKDLD
          EGSPVLLNCLMYKMCYYRFGQVYTEAKRPPGFDRVRNAEIGNKDFELDVLEEAYTTEHWLVRIYKVKDLD
Retrocopy EGSPVLLNCLMYKMCYYRFGQVYTEAKRPPGFDRVRNAEIGNKDFELDVLEEAYTTEHWLVRIYKVKDLD

Parental  NRGLSRT
          NRGLSRT
Retrocopy NRGLSRT

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	0.22 RPM	19.54 RPM
SRP017611_kidney	0.61 RPM	53.11 RPM
SRP017611_liver	1.39 RPM	60.12 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_684 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_684 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_684 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000014677	1 retrocopy	retro_ocun_684 ,
Ictidomys tridecemlineatus	ENSSTOG00000020526	1 retrocopy	retro_itri_546,