RetrogeneDB ID: retro_pabe_2845

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:28880730..28882265(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IQCB1
• Ensembl ID: ENSPPYG00000013494
• Aliases: None
• Description: IQ motif containing B1 [Source:HGNC Symbol;Acc:28949]

Sequence

>retro_pabe_2845
GAAGTTAAAAGCCATTGCTGTGCAGGCTTGGAGCCAGGAGAAGATGCAGAGGAACTTTTCAATGAATTACTTCCATCAGC
TGCAGAAAATTTTCTAGTTTTGGGGAGACAATAACAAATATGTTTTATCAATGCAGCTAAGGCTGAAGAAAAAGATGAGT
TACTACAAATTGTGACTGACTGGCTCTTCTGGCTTTTGGGAGGCCATGTTGAACTTATTCAGAATGTACTACAAAGTGAT
CATTTCTTACACTTACTGCAAGCTGACAATGTCCAAATAGGATCTGCACTCATGATGATGCTACAGAATATACTATAGAG
CAACAGTGGTGATTTACTCAGAACAGGAGGGAAAGCCCTGCATTCAATTTTAGATGAAGTTATTTTCAAGCTTTTTTCAG
CTCCTAGTCCAGTCATAAGAAGTACTGCTGCAAAACTCCTACTGTTGATGGCTGAATCCCATCAGGAAATTTTGATTTTA
CTGAGACAAAATGCCTGCTACAAAGGACTCAGAAGTCTACTAAGTAAACAGGAAACTGGGACAGAATTCAGTCAAGAACT
TAGACAGCTCATTGGCCTTTTAAGCCCAACGGTCTATCAGGAAGTAGAAGAGCAGAAACTACATCAAGCAGCCAACTTGA
TTCAAGCCTATTGGAAGGGTTTTCAGAGAAGAAAGAGATTAAAGAAGCTTCCATCTGCTGTGATTGCTTTGCAGAGGAGT
TTCAGATCTAAACAAACACAGATGTTGCTGGAGATAAATAGGCAGAAGGAAGAAGAGGACCTCAGATTGCGATCACAGCT
TCAAAGACAGAGAGCCATGAGACTTTCCCAAGAATTGCGGCTGAGTATGCTCAAAGTAGTTCATCCAGGTCAAGTGGAGA
AACACAATTGGGAAATGGAAGACAAATCAGCACTGATTATCCAGAAACATTGGAGACGGTACGGGGAAAGGAAAAATTTT
TGCCAACAGAGGCAGTCTCTTACAGAATATAAAGCAGCTGTCACACTTCAAAGAGCAGTGCTTAAATTCCTAGCAAAGTG
CCGTAAGAAACAGAAACTATTTGTTCCTTGGCGAGGACTCCAAGAACTCACTGATGCATGCTGAGTTGAACTGAAGCAAC
AAGTGGATGACTATGTCAGAAGACATTTGGGCTCTCCAACGTCAGATGTGGTCAGTAGGGAGCTCCATGCCCAAGCTCAA
GAATGACTGCAACACTACTTTATGGGCTGGGCCCTGGAAGAGTGAGCCCAGCAATACAGAGAAGCTCTGATGGTACAGAT
CAGCACCAACGTTGAACAGCTAATGAAGGCACCAAGTCTGAAGGAAGCAGAAGGGAAAGAACCTGAGCTTTTCCTAAGTA
GATCCAGGCCTGTGACAGCCAAGGCCAAGCAGGCCCATCTCACCACCCTGAAGCAGATACAACCCACACTGGTGGAAGAA
GCTTGGGGAAAGAATCTGGAGATGAGGTTGATGTTCCAAAGGATGAGCTTAGTGTGGAATTAGAAATTTTATTCATTGGT
GTAACCAAACCACCT

Alignment

ORF - retro_pabe_2845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.4 %
• Parental protein coverage: 85.95 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QILSHCCVGLEPGEDAEEFYNELLPSAAENFLVLGRQLQTCFINAAKAEEKDELLHFFQIVTDSLFWLLG
          ...SHCC.GLEPGEDAEE..NELLPSAAENFLVLGRQ.Q.CFINAAKAEEKDELL...QIVTD.LFWLLG
Retrocopy EVKSHCCAGLEPGEDAEELFNELLPSAAENFLVLGRQ*QICFINAAKAEEKDELL---QIVTDWLFWLLG

Parental  GHVELIQNVLQSDHFLHLLQADNVQIGSAVMMMLQNILQINSGDLLRIGRKALYSILDEVIFKLFSTPSP
          GHVELIQNVLQSDHFLHLLQADNVQIGSA.MMMLQNIL..NSGDLLR.G.KAL.SILDEVIFKLFS.PSP
Retrocopy GHVELIQNVLQSDHFLHLLQADNVQIGSALMMMLQNIL*SNSGDLLRTGGKALHSILDEVIFKLFSAPSP

Parental  VIRSTATKLLLLMAESHQEILILLRQSTCYKGLRSLLSKQETGTEFSQELRQLIGLLSPTVYQEVEEQKL
          VIRSTA.KLLLLMAESHQEILILLRQ..CYKGLRSLLSKQETGTEFSQELRQLIGLLSPTVYQEVEEQKL
Retrocopy VIRSTAAKLLLLMAESHQEILILLRQNACYKGLRSLLSKQETGTEFSQELRQLIGLLSPTVYQEVEEQKL

Parental  HQAACLIQAYWKGFQTRKRLKKLPYAVIALQRSFRSKRSKMLLEINRQKEEEDLKLQLQLQRQRAMRLSR
          HQAA.LIQAYWKGFQ.RKRLKKLP.AVIALQRSFRSK...MLLEINRQKEEEDL.L..QLQRQRAMRLS.
Retrocopy HQAANLIQAYWKGFQRRKRLKKLPSAVIALQRSFRSKQTQMLLEINRQKEEEDLRLRSQLQRQRAMRLSQ

Parental  ELQLSMLEIVHPGQVEKLYREMEEKSALIIQKHWRGYRERKNFHQQRQSLIEYKAAVTLQRAALKFLAKC
          EL.LSML..VHPGQVEK...EME.KSALIIQKHWR.Y.ERKNF.QQRQSL.EYKAAVTLQRA.LKFLAKC
Retrocopy ELRLSMLKVVHPGQVEKHNWEMEDKSALIIQKHWRRYGERKNFCQQRQSLTEYKAAVTLQRAVLKFLAKC

Parental  RKKKKLFAPWRGLQELTDAHRVELKKQVDDYVRRHLGSPMSDVVSRELHAQAQERLQHYFMGRALEERAQ
          RKK.KLF.PWRGLQELTDA..VELK.QVDDYVRRHLGSP.SDVVSRELHAQAQE.LQHYFMG.ALEE.AQ
Retrocopy RKKQKLFVPWRGLQELTDAC*VELKQQVDDYVRRHLGSPTSDVVSRELHAQAQE*LQHYFMGWALEE*AQ

Parental  QHREALMVQISTNVEQLMKAPSLKEAEGKEPELFLSRSRPVAAKAKQAHLTALKHIQAP-WWKKLGE-ES
          Q.REALMVQISTNVEQLMKAPSLKEAEGKEPELFLSRSRPV.AKAKQAHLT.LK.IQ...WWKKLGE.ES
Retrocopy QYREALMVQISTNVEQLMKAPSLKEAEGKEPELFLSRSRPVTAKAKQAHLTTLKQIQPT>WWKKLGE>ES

Parental  GDEIDVPKDELSIELETLFIGGTKPP
          GDE.DVPKDELS.ELE.LFIG.TKPP
Retrocopy GDEVDVPKDELSVELEILFIGVTKPP

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.54 RPM
SRP007412_cerebellum	0.12 RPM	9.24 RPM
SRP007412_heart	0.03 RPM	3.19 RPM
SRP007412_kidney	0.03 RPM	4.34 RPM
SRP007412_liver	0.06 RPM	2.91 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2845 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2845 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2845 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3441
Pan troglodytes	retro_ptro_2333
Gorilla gorilla	retro_ggor_2324

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000173226	1 retrocopy	retro_hsap_3441,
Gorilla gorilla	ENSGGOG00000028124	1 retrocopy	retro_ggor_2324,
Otolemur garnettii	ENSOGAG00000004271	1 retrocopy	retro_ogar_3056,
Pongo abelii	ENSPPYG00000013494	1 retrocopy	retro_pabe_2845 ,
Pan troglodytes	ENSPTRG00000015281	1 retrocopy	retro_ptro_2333,