RetrogeneDB ID: retro_ogar_2046

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873584.1:10585817..10586657(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000025928
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPA
• Ensembl ID: ENSOGAG00000002864
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide A [Source:HGNC Symbol;Acc:11151]

Sequence

>retro_ogar_2046
ATGGCAGTTCCAGAGGCCTGCCCCAACCACATTATTTATATCAACAACCTCTATGAGAAGATCAAAAAGGATGAGCTGAA
GAAGTCCCGGTATTCCATCTTCTCCCAGTCTGGCCAGATCCTGGATATCCTGGTATCACGAAGACTGGAGATGAGGGGCC
AGGCCTTGGTTATTTTTTAAGGTCAGTCGTGCCACCAATGCCCTTCGCTCCATGCAGGGTTCCCCATTTTATGACAAGCC
CATGTGCATCCAGTATGCCAAGACTGACTCAGATATCATCGTCAAGATGAAGGCCACCTTTGTGGAACAGGACTGCAAGT
GGGAGAAGAGGAAGCCCAAGAGGCTGGAGACCCCTCTGCCAAGAAGGCCATGCAGGGTGGGGCAGCTGCTTCCATGGTGG
GGGCTGTCCAGGGGCCTGTCCTGGGCATGCCTTCCATGACACAGGCACCCTGCATCATGCACCACATGCCAGGCCAGCCG
CCCTACATGCCGCCTCCTGGCATGATCGCACTGCCAGGGCTTGCCCAGCCAGATCCCACCAGGGGCCATGCCCCCACGGT
AGCTTAGCCTGGGCAGATGCCACCTGGCCAGCCTCTTTCTGAGAACCCACCGAATCACATTTTGTTTCTCACCAAGCTGC
CAGAGGAGACAGATGATCTCATACTGTCCATGCTTTTCAACCAGTTCCCTGGCTTCAAGGAGGTCCGCCTGGTGTCAGGG
CGGCATGACATCACCTTTATGGAGTTAGACAATGAGGTGCAGGCAGGGGCAGTTCGGAATGCTCTTCAAGGCTTTAAGAT
CACCCAGAACAATGCCATGAAGATCTCCTTTGCCAAGAAA

Alignment

ORF - retro_ogar_2046 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAVPEARPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVI-FKEVSSATNAL
          MAVPEA.PNH.IYINNL.EKIKKDELKKS.Y.IFSQ.GQILDILVSR.L.MRGQA.VI.FK.VS.ATNAL
Retrocopy MAVPEACPNHIIYINNLYEKIKKDELKKSRYSIFSQSGQILDILVSRRLEMRGQALVI>FK-VSRATNAL

Parental  RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETP-SAKKAVQGGAAAPVVGAVQ
          RSMQG.PFYDKPM.IQYAKTDSDII.KMK.TFVE.D.K.EKRKPK..ETP.SAKKA.QGGAAA..VGAVQ
Retrocopy RSMQGSPFYDKPMCIQYAKTDSDIIVKMKATFVEQDCKWEKRKPKRLETP<SAKKAMQGGAAASMVGAVQ

Parental  GPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPP-GLAPGQIPPGAMPPQQLM-PGQMPPAQPLSENPP
          GPV.GMP.MTQAP.IMHHMPGQPPYMPPPGMI..P.GL.P.QIPPGAMPP..L..PGQMPP.QPLSENPP
Retrocopy GPVLGMPSMTQAPCIMHHMPGQPPYMPPPGMIALP>GL-PSQIPPGAMPPR*LS<PGQMPPGQPLSENPP

Parental  NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMK
          NHILFLT.LPEET..L.LSMLFNQFPGFKEVRLV.GRHDI.F.E.DNEVQAGA.R.ALQGFKITQNNAMK
Retrocopy NHILFLTKLPEETDDLILSMLFNQFPGFKEVRLVSGRHDITFMELDNEVQAGAVRNALQGFKITQNNAMK

Parental  ISFAKK
          ISFAKK
Retrocopy ISFAKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2046 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005091	1 retrocopy	retro_cfam_1114,
Callithrix jacchus	ENSCJAG00000014865	1 retrocopy	retro_cjac_287,
Cavia porcellus	ENSCPOG00000010875	1 retrocopy	retro_cpor_663,
Myotis lucifugus	ENSMLUG00000000219	1 retrocopy	retro_mluc_1517,
Monodelphis domestica	ENSMODG00000007912	1 retrocopy	retro_mdom_447,
Mustela putorius furo	ENSMPUG00000017681	1 retrocopy	retro_mputfur_593,
Mus musculus	ENSMUSG00000061479	6 retrocopies	retro_mmus_275, retro_mmus_3374, retro_mmus_469, retro_mmus_888, retro_mmus_889, retro_mmus_958,
Otolemur garnettii	ENSOGAG00000002864	1 retrocopy	retro_ogar_2046 ,
Otolemur garnettii	ENSOGAG00000015146	1 retrocopy	retro_ogar_2042,
Pteropus vampyrus	ENSPVAG00000001494	1 retrocopy	retro_pvam_832,