RetrogeneDB ID: retro_itri_1822

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393911.1:166930..168103(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APBB2
• Ensembl ID: ENSSTOG00000009171
• Aliases: None
• Description: amyloid beta (A4) precursor protein-binding, family B, member 2 [Source:HGNC Symbol;Acc:582]

Sequence

>retro_itri_1822
GAGGATTTGCATGCAGCCACAGTTAATCCAGACCCCAGTTTAAAAGAGTTCGAAGAAGCAACGCTACGTTATGCATCTTT
GAAACTCAGAAATGTCCATCATGCTGATGATGATGATTCTTGTAGTATCAACAGTGACCCAGAAGCCAAGTGTTTCACTG
TGCGCTCTCTGGGATGGGTAGAGATGGCAGAGGAGGACCTCGCCCCTGGTAAAAGCAGCGTTGCTGTCAACAACTGCATC
AGGCAGCTCTCTTACTGCAAAAATGACATCCGAGATACAGTTGGCATTTGGGGAGAAGGCAAAGACATGTACCTGATACT
GGAGAACAACATGCTCAGCCTGGTCAACCCCATGGACCGCACAGCGCTGCACTCACAGCCCATCATGAGCATCCATGTGT
GGGGCGTGGGCCGCGACAATGGCCGGGATTTTGCTTATGTAGCAAGAGATAAAGATACCAGAATTTTGAAATGTCATGTA
TTTCGATGTGACACACCAGCAAAAGTCATTGCCACAAGTCTCCACGAAATTTGTTCCAAGATTATGGCTGAACAGAAGAA
TGCAAAAGCCCTGGCCTGCAGCTCCTTTCAGGAGAGGACCAGTGTGAATCCCGAAGTCCCTTTGCAAGTAGATTTTCCAA
TGCCAAAGACTGAACTGGTCCAGAAGTTCCACATGCAGTACTTGGGCATGTTACCTGTCGACAAACCAGTTGGAATGGAC
ATCCTGAACAATGCCATAGAAAGTCTAATGACCTCATCTAACAAGGAGGATTGGCCATCAGTGAACATGAATGTGGCCGA
TGCCACTGTGACGGTCATCAGTGAAAAGAATGAAGAGGAGACCTTGGTGGAGTGCCGGGTGTGATTCCGGTCCTTCATGG
GTATCGGGAAGGATGTCCACACGTTTGCCTTCATCATGGACACTGGGAACCAGTGCTTTGAGTGCCACGTGTTCTGGTGC
GAGCCCAATGCTGGTAATGTGTCGGAGGCGGTCCAGGCCGCCTGCATGTTACAATATCAGAAGTGCTTGGTAGCCCGGCC
ACCTTCACAGAAAGTTCGACCACCTCCTCCGCCTGCAGACTCAATGACCAGAAGAGTCACAACCAATGTAAAACTAGGAG
TCTTATTCCTCATTGACACTTTGAAACAGAAACTTCCTGTCACAGAAACACCC

Alignment

ORF - retro_itri_1822 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.61 %
• Parental protein coverage: 51.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDLHAATVNPDPSLKEFEGATLRYASLKLRNVPHADDDDSCSINSDPEAKCFAVRSLGWVEMAEEDLAPG
          .DLHAATVNPDPSLKEFE.ATLRYASLKLRNV.HADDDDSCSINSDPEAKCF.VRSLGWVEMAEEDLAPG
Retrocopy EDLHAATVNPDPSLKEFEEATLRYASLKLRNVHHADDDDSCSINSDPEAKCFTVRSLGWVEMAEEDLAPG

Parental  KSSVAVNNCIRQLSYCKNDIRDTVGIWGEGKDMYLILENDMLSLVDPMDRTVLHSQPIVSIRVWGVGRDN
          KSSVAVNNCIRQLSYCKNDIRDTVGIWGEGKDMYLILEN.MLSLV.PMDRT.LHSQPI.SI.VWGVGRDN
Retrocopy KSSVAVNNCIRQLSYCKNDIRDTVGIWGEGKDMYLILENNMLSLVNPMDRTALHSQPIMSIHVWGVGRDN

Parental  GRDFAYVARDKDTRILKCHVFRCDTPAKAIATSLHEICSKIMAERKNAKALACSSSQERTSVNPEVPLQV
          GRDFAYVARDKDTRILKCHVFRCDTPAK.IATSLHEICSKIMAE.KNAKALACSS.QERTSVNPEVPLQV
Retrocopy GRDFAYVARDKDTRILKCHVFRCDTPAKVIATSLHEICSKIMAEQKNAKALACSSFQERTSVNPEVPLQV

Parental  DFPTPKTELVQKFHVQYLGMLPVDRPVGMDTLNSAIESLMTSSNKEDWPSVNMNVADATVTVISEKNEEE
          DFP.PKTELVQKFH.QYLGMLPVD.PVGMD.LN.AIESLMTSSNKEDWPSVNMNVADATVTVISEKNEEE
Retrocopy DFPMPKTELVQKFHMQYLGMLPVDKPVGMDILNNAIESLMTSSNKEDWPSVNMNVADATVTVISEKNEEE

Parental  TLVECRVRFLSFMGVGKDVHTFAFIMDTGNQRFECHVFWCEPNAGNVSEAVQAACMLRYQKCLVARPPSQ
          TLVECRV.F.SFMG.GKDVHTFAFIMDTGNQ.FECHVFWCEPNAGNVSEAVQAACML.YQKCLVARPPSQ
Retrocopy TLVECRV*FRSFMGIGKDVHTFAFIMDTGNQCFECHVFWCEPNAGNVSEAVQAACMLQYQKCLVARPPSQ

Parental  KVRPPPPPADSMTRRVTTNVKRGVLSLIDTLKQKRPVTETP
          KVRPPPPPADSMTRRVTTNVK.GVL.LIDTLKQK.PVTETP
Retrocopy KVRPPPPPADSMTRRVTTNVKLGVLFLIDTLKQKLPVTETP

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1822 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1822 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000009171	1 retrocopy	retro_itri_1822 ,